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@Jean-Romain Jean-Romain released this 09 Jun 10:15
· 737 commits to master since this release
v3.0.0
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lidR v3.0.0 (Release date: 2020-06-08)

MAJOR CHANGES

Summary

In lidR version 3.0.0, 80% of the functions were renamed. Old functions were soft-deprecated, meaning that they still exist so version 3 is fully compatible with version 2, at least for 1 year. Users should start to use the new names. See ?lidR::deprecated for the list of deprecated functions and their new names. The plan is to remove these functions in 1 year so they will progressively print a message, then throw a warning, then throw an error, after which they will be definitively removed.

Full explanation

At the very beginning of the development of lidR we started to name the functions that return a LAS object lassomething(). At that point there were 5 functions and ~10 users. As lidR grew up, we kept going with this naming convention but now lidR is used worldwide and this naming convention now overlaps with the LAStools software suite created by Martin Isenburg. This creates confusion for users which is problematic both for Martin and for us. This situation is likely to get worse as more tools are released into LAStools. We discussed the issue with Martin Isenburg and we took the decision to rename the functions in the lidR package so that the overlaps in namespace will progressively disappear.

The new naming convention follows the currently trending verb_noun syntax initiated by the tidyverse. For example, lasnormalize() becomes normalize_height(), while lasground() becomes classify_ground(). The full list of changes can be found in ?lidR::deprecated.

In efforts to avoid breaking users' scripts version 3 is fully backwards-compatible. For example, the function lasground() still exists and can be used without throwing a warning or error message. But this will progressively change with versions 3.1.0, 3.2.0 and 3.3.0. First a message will be displayed to invite users to change to using the new names, then a warning, then finally an error. After a year, maybe 18 months, the function will no longer exist. So users are invited to adopt the new naming convention as soon as possible.

NEW FEATURES

  1. readLAScatalog() has new parameters to tune the processing options at read time without using the functions opt_*().

    readLAScatalog("folder/", chunk_buffer = 60, filter = "-drop_z_below 2")

  2. New function clip_transect() to extract a transect between two points. The function has the capability to reorient the point cloud to put it on XZ coordinates and easily create some 2D rendering of the transects in e.g. ggplot2.

  3. New function readMSLAS() to read multisprectral data from 3 different files.

    readMSLAS("channel1.las", "channel2.las", "channel3.las", filter = "-keep_first")

  4. delineate_crowns() (formerly named tree_hulls()) now returns 3 metrics: XTOP, YTOP and ZTOP, that contain the coordinates of the apices of the trees.

  5. segment_trees() (formerly named lastrees()) and find_trees() (formerly tree_detection()) can now perform the computation on a LAScatalog using two strategies to ensure that tree IDs are always unique on a coverage and that trees that belong on the edge of two tiles will independently get the same IDs.

  6. point_metrics()

    • supports a knn neighborhood search with missing r and given k
    • supports a spherical neighborhood search with missing k and given r
    • supports a knn neighborhood + a radius limit with k and r given
    • default setting is now xyz = FALSE
    • if xyz = FALSE the the output now contains a column (the first one) named pointID that references the point of the original las object. See #325

  7. normalize_height() (formerly named lasnormalize())

    • new argument add_lasattribute. If TRUE the absolute elevation (above sea level) is retained as before, but the header is updated so the absolute elevation becomes an extrabyte attribute writable on a las file. Otherwise the information is discarded at write time.
    • new argument Wdegenerated. If FALSE the function does not warn about degenerated points. Degenerated points are removed anyway.

  8. New function find_localmaxima() to find local maxima with different windows. This function is designed for programming purposes, not to find individual trees. This latter task is still performed by find_trees() (formerly called tree_detection()). Instead, find_localmaxima() may help with finding other human-made structures.

  9. Internal global variables were exported to help with ASPRS LAS classification standard. Instead of remembering the classification table of the specification it is now possible to use one of LASNONCLASSIFIED, LASUNCLASSIFIED, LASGROUND, LASLOWVEGETATION, LASMEDIUMVEGETATION, LASHIGHVEGETATION, LASBUILDING, LASLOWPOINT, LASKEYPOINT, LASWATER, LASRAIL, LASROADSURFACE, LASWIREGUARD, LASWIRECONDUCTOR, LASTRANSMISSIONTOWER, LASBRIGDE, LASNOISE. e.g.:

    filter_poi(las, !Classification %in% c(LASWIRECONDUCTOR, LASTRANSMISSIONTOWER))

  10. The internal function catalog_makechunks() has been exported. It is not actually intended to be used by regular users but might be useful in some specifc cases for debugging purposes.

  11. lasmetrics(), grid_metrics3d(), grid_hexametrics() were deprecated in previous versions. They are now defunct.

  12. las_check() (formerly named lascheck()):

    • gains an option print = FALSE.
    • now returns a list for further automatic processing/parsing. If print = TRUE the list is returned invisibly so the former behavior looks the same.
    las_check(las, FALSE)
#> $warnings
#> [1] "1 points are duplicated and share XYZ coordinates with other points"                                         
#> [2] "There were 1 degenerated ground points. Some X Y Z coordinates were repeated."                               
#> [3] "There were 1 degenerated ground points. Some X Y coordinates were repeated but with different Z coordinates."
#> 
#> $errors
#> [1] "Invalid header: X scale factors should be factor ten of 0.1 or 0.5 or 0.25 not 0.123"                      
#> [2] "Invalid file: the data contains a 'gpstime' attribute but point data format is not set to 1, 3, 6, 7 or 8."
    • gains an option deep = TRUE with a LAScatalog only. In this case it performs a deep inspection of each file reading each point cloud.
    • the coordinates of the points are expected to be given with a resolution e.g. 0.01 meaning a centimetre accuracy. It means we are expecting values like 12345.67 and not like 12345.6712. This is always the case when read from a LAS file but users (or lidR itself) may transform the point cloud and generate LAS objects where this rule is no longer respected. lidR always ensures to return LAS objects that are stricly valid with respect to ASPRS standard. If not valid this may lead to failure in lidR because some functions, such as tin(), dsmtin(), pitfree() work with the integer representation of the coordinates. This is why we introduced a quantization check in las_check().
    • now reports problems for invalid data reported in #327

  13. merge_spatial() (formerly named lasmergespatial()) now supports sf POLYGON objects.

  14. plot()

    • for LAS object gains an argument add to overprint two point clouds with e.g. different color palettes #325.
    las = readLAS("classified.las")
nonveg = filter_poi(las, Classification != LASHIGHVEGETATION)
veg = filter_poi(las, Classification == LASHIGHVEGETATION)
x = plot(nonveg, color = "Classification")
plot(veg, add = x)
    • for LAScatalog objects gains an argument overlaps = TRUE to highlight the overlaps.

  15. New function add_lasrgb() to add RGB attributes. The function updates the header in such a way that the LAS object has a valid point format that supports RGB.

  16. LAScatalog processing engine

    • gains a generic option opt_merge(ctg) <- FALSE to disable final merging and force the engine to return a list
    • gains a generic option opt_independent_files(ctg) <- TRUE to set adequate options to a collection of independent files, for example a set of circular ground inventory plots. It is equivalent to set no buffer, processing by file and no wall-to-wall guarantee.
    • gains an option autoread = TRUE in catalog_apply(). Not actually intended to be used widely but might be convenient for some use cases.

  17. New function get_range().

  18. knnidw() gains an argument rmax to set a maximum radius search in which to find the knn. This fixes computation time issues with non-convex point clouds.

  19. track_sensor() (formerly sensor_tracking())

    • now has two available algorithms.
    • supports systems with multiple pulses emission which formerly failed

  20. writeLAS() gains a parameter index = TRUE to automatically write a lax file along with the las/laz file.

ENHANCEMENTS

  1. readLAS() now warns when reading incompatible files. Point coordinates are recomputed on-the-fly as it has always been done but now the user is aware of potential problems or precision loss.

  2. A new vignette named LAScatalog processing engine has been added and documents in-depth the catalog_apply() engine of lidR.

  3. In clip_*() several lines of codes were removed because they were not used. We suspected these lines covered old cases from lidR v1.x.y that are no longer relevant. If a user encounters problems, please report.

  4. The arguments select and filter from readLAS() are not expected to be used with a LAScluster when processing a LAScatalog. The options are carried by the LAScatalog itself with opt_select() and opt_filter(). If used, a warning is now thrown.

  5. Enhancements made here and there to improve the support of the CRS when reading and checking a LAS file.

  6. When processing by file with a raster output, automatic chunk extension to match with a raster resolution now performs a tighter extension.

  7. Minor modification of print() methods to enhance information displayed.

  8. All algorithms such as tin(), p2r(), knnidw(), li2012(), and so on, now have the classes c("lidRAlgorithm", "something") and a dedicated print function. The source code is no longer displayed when printing these objects

    f = lmf(2)
f
#> Object of class lidR algorithm
#> Algorithm for: individual tree detection 
#> Designed to be used with: find_trees 
#> Native C++ parallelization: yes 
#> Parameters: 
#>  - circ = TRUE <logical>
#>  - hmin = 2 <numeric>
#>  - shape = circular <character>
#>  - ws = 2 <numeric>

  9. In grid_metrics() the RasterBrick is built much faster.

FIXES

  1. In delineate_crowns(), formerly named tree_hull(), when applied to a LAScatalog the buffer was not properly removed. The polygons were simply clipped using the bounding box of the chunk. Now the trees that have an apex in the buffer are removed and the trees that have an apex outside the buffer are retained. Thus, when merging, everything is smooth and continuous.

  2. catalog_retile() returns a LAScatalog with only the newly created files even if the folder contains other las files. It formerly read every las file in the folder leading to an invalid catalog if the folder already contained las files.

  3. Previously in automatic filename generation the template YCENTER was not actually recognized. However, XCENTER was recognized but actually contained the value for YCENTER. This was working for lasclip() thanks to a previous fix but was still a problem in other functions when processing chunks.

  4. Function wkt() no longer masks the new function wkt() in sp.

  5. merge_spatial() (formerly named lasmergespatial()) no longer fails with a LAS object containing a single point.

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