Fix: The local_maximum function previously experienced significant delays when writing points to disk, taking up to 2 seconds on Linux and up to 30 seconds on Windows. This issue severely hindered parallelization capabilities. The new fix dramatically reduces the write time to around 0.1 seconds, greatly improving overall performance.
stop_if() before reader_las(). Previously, the buffer was being read even when points were meant to be skipped, leading to unnecessary processing time (a few seconds per skipped file).classify_with_sor() to classify outliers with statistical outlier removal.focal() to post-process rasters in the pipeline.filter_with_grid() to keep the lowest or highest point per cell of a grid.geometry_feature, r = 5 was equal to 5 but r = 4.5 was equal to 4.region_growing() for individual tree segmentation were inverted.-keep_last, -keep_class 128) are now functional with LAS 1.4..copc.las extension; .copc is automatically discarded.classify_with_csf() stage has gained a filter argument.load_raster() if the raster does not have an extent that overlaps with the point cloud.sort() now handles duplicated gpstime properly.local_maximum() could return multiple too-close local maximum points if two close points have the exact same Z coordinates and the exact same X or Y coordinates (but not both X and Y; duplicated points were properly handled). This particularly affected local_maximum_raster(), where two pixels can easily have the same Z and the same X or Y.region_growing() the th_tree argument was not properly respected.transform_with with a TIN won't fail if there is no TIN. Instead all points will be removed.exec() accepts the path to a json file produced by a UI (non documented)keep_ground_and_water()normalize uses keep_ground_and_water()triangulation fails with < 3 pointssort_points() to optimize compression.write_lax() is 2x faster when used as a single stagewrite_lax() for LAS 1.4.write_lax() is now parallelizeduse_gpstime in write_vpc()write_vpc()write_vpc() writes valid files readable by QGISivf is faster.New stage classify_with_csf() to classify ground points.
The metric engine introduced in v0.6.0 can now compute metrics on extrabytes attributes. e.g. Amplitude_mean
New stage sampling_poisson to perform Poisson Disk Sampling
sampling_pixel and sampling_voxel are faster.
sampling_* stages respect the filter argument
Fix #63 crash when some chunk are skipped either because they have 0 points of because of the stop_if stage.
Fix #64 metrics on RGB were actually computed on RRR
classify_isolated_voxels() renamed into classify_with_ivf() for consistency.*cv and sd that were not computed properly.cv and sd that return NAs instead of Inf in the edges case where they are undefined.reader_las() stage. It now displays the correct percentage.write_las() without wildcard (merge mode) works with files that have different formats and scales/offsetsNew stage stop_if to conditionally escape the pipeline. New section about stop_if in the online tutorial.
New stage write_lax. This stage was automatically added by the engine but can now be explicitly added by users.
New internal "metric engine". The metric engine is used to compute metrics in, e.g., rasterize() with operators like zmean, imean, and so on. The metric engine has been redesigned and allows any string with the format attribute_metric such as z_sd, i_mean, c_mode, a_mean, intensity_max, classification_mode, angle_mean, and any other combinations. All attributes are mapped, and new functions are available such as sum, mode. Many more could be added easily. Former strings such as zmean or imax are no longer valid and should be replaced by z_mean and i_max but are backward compatible.
rasterize gained access to the new metric engine and can compute many more metrics natively.
summarize() gained access to the metric engine and can compute metrics for each file or each chunk. Used in conjunction with reader_las_circle(), it can be used, for example, to compute plot inventory metrics. The online tutorial has been updated. The section "plot inventory" no longer uses callback() and is preceded by a new section "summarize".
The package no longer assigns set_parallel_strategy(concurrent_points(half_core())) when loading. Instead, if nothing is provided, this is interpreted as concurrent_points(half_core()). Thus, users can now write exec(pipeline, on = file, ncores = 8). The engine will now respect ncores = 8 because no global settings with global precedence were assigned. The multi-threading vignette has been updated.
Pipelines that include R-based stages (rasterize with R function, callback) are no longer parallelizable with the concurrent-file strategy. Parallelizing a pipeline that involves the R C API is terribly complex and eventually leads only to pseudo-parallelism with a lot of troubleshooting to deal with (especially to abort the pipeline). Consequently, we removed parallelism capabilities. The numerous new native metrics added in the metric engine compensate for that loss. The online documentation has been updated accordingly.
lasR from R. lasR can now be compiled as standalone software. A Makefile has been added to the repository. At the R level, the pipeline and the processing options are passed to the C++ engine via a JSON file instead of being passed via the R's C API, effectively separating lasR from R itself. The R side of lasR is now purely an API to the standalone engine. A JSON file produced by the lasR package can be executed with the standalone software: lasr pipeline.json. However, the syntax of the JSON file is not documented and is not intended to be documented. Rather, the JSON file should be produced by an API such as the lasR package, a QGIS plugin, or a Python package. Obviously, there is currently no such thing.reader_las() with COPC files, depth query (-max_depth), and buffer. The depth query was not performed at all. The fix is temporary: it breaks the progress bar of reader_las() but this is a less serious bug.reader_las() with very large files.load_raster() is thread-saferasterize() accepts a new argument default_value. When rasterizing with an operator and a filter (e.g. -keep_z_above 2) some pixels that are covered by points may no longer contain any point that pass the filter criteria and are assigned NA. To differentiate NAs from non covered pixels and NAs from covered pixels but without point that pass the filter, the later case can be assigned another value such as 0.write_vpc() properly reprojects the bounding boxes in WGS84write_vpc() writes zmin and zmax for each file.local_maximum() no longer fails with ofile = ""reader_las() for COPC files.zsd and isd were incorrect due to wrong parenthesis in the code.delete_points() when 0 points left.list.list returned by exec is named and duplicated names are made unique with make.names()geometry_features() to address question in #45set_crs() no longer forces the pipeline to read the files.exec() normalizes the path so users do not get an error when providing a path with a ~.rasterize() gained a metric zaboveX to compute canopy cover.geometry_features after delete_points()local_maximum() was processing deleted points.write_vpc write the datetimedelete_points can now physically remove the deleted points if the number of points deleted is important. Before they were flagged but kept in memory. It can also free available memory.write_vpc() gained an argument absolute_pathwrite_vpc() orders the long/lat coordinates properly on Linuxwrite_vpc() writes the absolute path of the relative path does not exist on Windowstriangulate() with 0 point chunk.geometry_feature works if the file already contains some extrabytes attributesdelete_points() removes all the points, the pipeline is stopped for the current chunk/file but the computation keep going for others. This was not the case for all stages and some stages could either crash or stop the computation.write_vpc() does not crash with files without CRSwrite_vpc() write the CRS set upstream by set_crs()geometry_features() to compute point wise geometry features based on k-nearest neighbors.callback() can load more than 10 extrabyte attributes. Using the flag E all the extrabytes are loaded.set_crs() to assign a coordinate reference system at some point of the pipeline.GeoTiff format are now created with COMPRESS=DEFLATE, PREDICTOR=2,TILED=YES effectively reducing the size of the rasterssummarize() output includes the CRS.local_maximum() gained a record_attributes argument to chose if the attribute of the points are recorded in the vector file.local_maximum_raster() no longer record zeroed LAS point attributeslax included into laz file were not working.rasterize() produced corrupted output.set_parallel_strategy(nested(ncores = 4, ncores2 = 4)).datatime is datetime in VPC files.write_vpc() writes the correct number of points for LAS 1.4 files.record_length_after_header).add_attribute() was incorrectly reallocating memory causing potential crashes, especially when adding several attributes.reader_las() crashing if the header of the LAS file did not record the correct number of points.local_maximum_raster.?multithreadinglocal_maximum_raster to compute local maximum on a rasterwith in exec to pass processing options that should be preferred over direct naming.set_exec_options() to assign global processing options and override arguments potentially hardcoded in exec()load_raster to read a raster instead of producing it on the fly from the point cloud.add_rgb to modify the point data format?multithreading?exec and ?set_exec_optionspoint_in_triangle.transform_with can be used with pit_fillpit_fill producing corrupted outputpit_fill was not respecting the parameters given by the userpit_fill in combination with rasterize("max") was not working properlylibrary(lasR) transparently checks for latest version on Windows.processor() and reader() are deprecated and are replaced by exec() and reader_las(). This intends to provide a more consistent and natural way to separate the pipeline. i.e the stages and the global processing options i.e. the buffer, the chunking, the progress bar. For example the following now respects the LAScatalog processing options and this was not possible with the previous syntax.
ctg = lidR::readLAScatalog()
pipeline = reader_las() + rasterize(...)
exec(pipeline, on = ctg)
lidR
pipeline = reader_las() + rasterize(...)
exec(pipeline, on = file, chunk = 500)
delete_points() to remove some points in the pipeline.dtm = dtm()
pipeline <- read + dtm + transform_with(dtm[[2]])
pipeline = rasterize(...)
exec(pipeline, on = ctg)
summarize(), rasterize() and write_las() no longer process withheld points in streaming mode.callback() properly handles errors from the injected functiontempxyz() to generate temp files with extension .xyz.rasterize() is now parallelized with internal metrics including for buffered area based approachrasterize() gained a progress bar with internal metrics.rasterize() gains the ability to perform a multi-resolution or buffered rasterization. See documentation.rasterize() gains numerous native metrics such as zmax, zmean, zmedian, imax, imean and so on.LAScatalog from lidR respecting the processed attribute used in lidRLAScatalog) can be enabled with progress = TRUEncores in processor(), which incorrectly mentioned that it was not supported.ncores() and half_cores().