Merge pull request #821 from r-lidar/nanoflann

Nanoflann

Author: Jean-Romain

.gitattributes

@@ -0,0 +1,5 @@
+# https://github.com/topepo/Cubist/blob/193c8b61933e2cef65658cf0e35aa25dcd25f3b6/.gitattributes
+# On GitHub Actions with Windows, git will use CRLF by default when checking out
+# the repo. If this file has CRLF line endings, R's check process will complain.
+
+configure.ac text eol=lf

.github/workflows/R-CMD-check.yaml

@@ -24,7 +24,7 @@ jobs:
         config:
           - {os: windows-latest, r: 'devel', rglusenull: "true"}
           - {os: windows-latest, r: 'release', rglusenull: "true"}
-          #- {os: macOS-latest, r: 'release', rglusenull: "true"}
+          - {os: macOS-latest, r: 'release', rglusenull: "true"}
           - {os: ubuntu-latest, r: 'release'}
           - {os: ubuntu-latest, r: 'devel'}
 
@@ -46,13 +46,9 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Brew and macOS config
-        if: runner.os == 'macOS'
-        run: |
-          # conflicts with gfortran from r-lib/actions when linking gcc
-          rm '/usr/local/bin/gfortran'
-          brew install gdal proj geos
-          brew install --cask xquartz
+      - name: Install macOS system dependencies
+        if: runner.os == 'macos'
+        run: brew install gdal proj
 
       - name: Query dependencies
         run: |
@@ -63,7 +59,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}

.gitignore

@@ -12,3 +12,6 @@ revdep
 CRAN-RELEASE
 /doc/
 /Meta/
+autom4te.cache
+config.log
+config.status

DESCRIPTION

@@ -2,9 +2,9 @@ Package: lidR
 Type: Package
 Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
     Applications
-Version: 4.1.3
+Version: 4.2.1
 Authors@R: c(
-    person("Jean-Romain", "Roussel", email = "[email protected]", role = c("aut", "cre", "cph")),
+    person("Jean-Romain", "Roussel", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("David", "Auty", email = "", role = c("aut", "ctb"), comment = "Reviews the documentation"),
     person("Florian", "De Boissieu", email = "", role = ("ctb"), comment = "Fixed bugs and improved catalog features"),
     person("Andrew", "Sánchez Meador", email = "", role = ("ctb"), comment = "Implemented wing2015() for segment_snags()"),
@@ -32,7 +32,7 @@ Imports:
     lazyeval,
     Rcpp (>= 1.0.3),
     rgl,
-    rlas (>= 1.5.0),
+    rlas (>= 1.8.2),
     sf,
     stats,
     stars,
@@ -55,8 +55,125 @@ Suggests:
     testthat (>= 2.1.0),
     knitr,
     rmarkdown
-RoxygenNote: 7.3.1
-LinkingTo: BH (>= 1.72.0),Rcpp,RcppArmadillo
+RoxygenNote: 7.3.2
+LinkingTo: BH (>= 1.72.0),Rcpp,RcppArmadillo,Rnanoflann
 Encoding: UTF-8
 ByteCompile: true
 VignetteBuilder: knitr
+Biarch: true
+Collate: 
+    'Class-LAS.R'
+    'Class-LAScatalog.R'
+    'Class-LAScluster.R'
+    'RcppExports.R'
+    'add_attribute.R'
+    'algorithm-dec.R'
+    'algorithm-dsm.R'
+    'algorithm-dtm.R'
+    'algorithm-gnd.R'
+    'algorithm-itd.R'
+    'algorithm-its.R'
+    'algorithm-noi.R'
+    'algorithm-out.R'
+    'algorithm-shp.R'
+    'algorithm-snag.R'
+    'algorithm-trk.R'
+    'backward_compatibility.R'
+    'catalog_apply.R'
+    'catalog_boundaries.R'
+    'catalog_fakerun.R'
+    'catalog_intersect.R'
+    'catalog_laxindex.R'
+    'catalog_overlaps.R'
+    'catalog_retile.R'
+    'catalog_select.R'
+    'classify.R'
+    'classify_ground.R'
+    'classify_noise.R'
+    'classify_poi.R'
+    'clip_roi.R'
+    'connected_components.R'
+    'decimate_points.R'
+    'io_readLAScatalog.R'
+    'io_readXLAS.R'
+    'deprecated.R'
+    'doc-drivers.R'
+    'doc-lidR.R'
+    'doc-parallelism.R'
+    'doc-spatialindex.R'
+    'engine.R'
+    'engine_apply.R'
+    'engine_chunks.R'
+    'engine_crop.R'
+    'engine_index.R'
+    'engine_merge.R'
+    'engine_options.R'
+    'engine_write.R'
+    'fasterize.R'
+    'filters.R'
+    'fit_shapes.R'
+    'fullwaveform.R'
+    'generate_las.R'
+    'io_readLAS.R'
+    'io_writeLAS.R'
+    'knn.R'
+    'las_check.R'
+    'las_compression.R'
+    'las_tools.R'
+    'locate_localmaxima.R'
+    'locate_trees.R'
+    'merge_spatial.R'
+    'methods-LAS.R'
+    'methods-LAScatalog.R'
+    'methods-LAScluster.R'
+    'methods-LASheader.R'
+    'metrics_cloud.R'
+    'metrics_crowns.R'
+    'metrics_hexagons.R'
+    'metrics_pixels.R'
+    'metrics_plot.R'
+    'metrics_point.R'
+    'metrics_polygon.R'
+    'metrics_stdmetrics.R'
+    'metrics_template.R'
+    'metrics_voxels.R'
+    'normalize.R'
+    'normalize_height.R'
+    'normalize_intensity.R'
+    'plot.R'
+    'plot.s3.R'
+    'plugins.R'
+    'print.R'
+    'rasterize.R'
+    'rasterize_canopy.R'
+    'rasterize_density.R'
+    'rasterize_terrain.R'
+    'retrieve_info.R'
+    'segment.R'
+    'segment_shapes.R'
+    'segment_snags.R'
+    'segment_trees.R'
+    'smooth_height.R'
+    'st_area.R'
+    'st_as_sf.R'
+    'st_bbox.R'
+    'st_coordinates.R'
+    'st_crs.R'
+    'st_hull.R'
+    'st_misc.R'
+    'st_transform.R'
+    'track_sensor.R'
+    'utils_assertive.R'
+    'utils_base.R'
+    'utils_chm.R'
+    'utils_colors.R'
+    'utils_constant.R'
+    'utils_delaunay.R'
+    'utils_geometry.R'
+    'utils_is.R'
+    'utils_misc.R'
+    'utils_raster.R'
+    'utils_spatial_index.R'
+    'utils_threads.R'
+    'voxelize_points.R'
+    'zzz.R'

NAMESPACE

@@ -171,6 +171,7 @@ export(LASheader)
 export(Roussel2020)
 export(VCI)
 export(add_attribute)
+export(add_circle3d)
 export(add_dtm3d)
 export(add_flightlines3d)
 export(add_lasattribute)
@@ -179,6 +180,7 @@ export(add_lasnir)
 export(add_lasrgb)
 export(add_treetops3d)
 export(as.spatial)
+export(barycenter_per_voxel)
 export(catalog)
 export(catalog_apply)
 export(catalog_boundaries)
@@ -197,6 +199,7 @@ export(clip_roi)
 export(clip_transect)
 export(cloud_metrics)
 export(concaveman)
+export(connected_components)
 export(count_not_quantized)
 export(crown_metrics)
 export(csf)
@@ -224,6 +227,7 @@ export(filter_poi)
 export(filter_single)
 export(filter_surfacepoints)
 export(find_trees)
+export(fit_circle)
 export(forest.colors)
 export(gap_fraction_profile)
 export(get_lidr_threads)
@@ -234,9 +238,10 @@ export(grid_metrics)
 export(grid_terrain)
 export(header)
 export(height.colors)
+export(height_above_ground)
 export(hexagon_metrics)
-export(hexbin_metrics)
 export(highest)
+export(highest_attribute_per_voxel)
 export(homogenize)
 export(index)
 export(interpret_waveform)
@@ -247,7 +252,10 @@ export(is.overlapping)
 export(is.parallelised)
 export(is.quantized)
 export(ivf)
+export(knn)
+export(knn_distance)
 export(knnidw)
+export(knnx)
 export(kriging)
 export(las_check)
 export(las_is_compressed)
@@ -256,46 +264,11 @@ export(las_reoffset)
 export(las_rescale)
 export(las_size)
 export(las_update)
-export(lasadddata)
-export(lasaddextrabytes)
-export(lasaddextrabytes_manual)
-export(lascheck)
-export(lasclip)
-export(lasclipCircle)
-export(lasclipPolygon)
-export(lasclipRectangle)
-export(lasdetectshape)
-export(lasfilter)
-export(lasfilterdecimate)
-export(lasfilterduplicates)
-export(lasfilterfirst)
-export(lasfilterfirstlast)
-export(lasfilterfirstofmany)
-export(lasfilterground)
-export(lasfilterlast)
-export(lasfilternth)
-export(lasfiltersingle)
-export(lasfiltersurfacepoints)
-export(lasflightline)
-export(lasground)
-export(lasmergespatial)
-export(lasnormalize)
-export(laspulse)
-export(lasrangecorrection)
-export(lasremoveextrabytes)
-export(lasreoffset)
-export(lasrescale)
-export(lasscanline)
-export(lassmooth)
-export(lassnags)
-export(lastrees)
-export(lasunnormalize)
-export(lasunsmooth)
-export(lasvoxelize)
 export(li2012)
 export(lmf)
 export(locate_trees)
 export(lowest)
+export(lowest_attribute_per_voxel)
 export(manual)
 export(mcc)
 export(merge_spatial)
@@ -350,19 +323,26 @@ export(range_correction)
 export(rasterize_canopy)
 export(rasterize_density)
 export(rasterize_terrain)
+export(readALS)
 export(readALSLAS)
 export(readALSLAScatalog)
+export(readALScatalog)
 export(readDAPLAS)
 export(readDAPLAScatalog)
 export(readLAS)
 export(readLAScatalog)
 export(readLASheader)
 export(readMSLAS)
+export(readTLS)
 export(readTLSLAS)
 export(readTLSLAScatalog)
+export(readTLScatalog)
 export(readUAVLAS)
 export(readUAVLAScatalog)
+export(remove_ground)
 export(remove_lasattribute)
+export(remove_noise)
+export(remove_water)
 export(retrieve_flightlines)
 export(retrieve_pulses)
 export(retrieve_scanlines)
@@ -371,7 +351,6 @@ export(segment_shapes)
 export(segment_snags)
 export(segment_trees)
 export(sensor)
-export(sensor_tracking)
 export(set_lidr_threads)
 export(shp_hline)
 export(shp_hplane)
@@ -397,8 +376,6 @@ export(storable_coordinate_range)
 export(template_metrics)
 export(tin)
 export(track_sensor)
-export(tree_detection)
-export(tree_hulls)
 export(tree_metrics)
 export(unnormalize_height)
 export(unsmooth_height)