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I have a point cloud with extra attributes:

class        : LAS (LASFˇ v1.4)
point format : 6
memory       : 2 Gb 
extent       :7498400, 7499200, 5779500, 5780000 (xmin, xmax, ymin, ymax)
coord. ref.  : NA 
area         : 399973.7 units² (convex hull)
points       : 19517984 points
density      : 48.8 points/units²
names        : X Y Z gpstime Intensity ReturnNumber NumberOfReturns ScanDirectionFlag EdgeOfFlightline Classification ScannerChannel Synthetic_flag Keypoint_flag Withheld_flag Overlap_flag ScanAngle UserData PointSourceID Amplitude Reflectance Deviation 
File signature:           LASFˇ 
File source ID:           4001 
Project ID - GUID:        df4425f5-d89d-437c-baa3-cd71726ed8c6 
Version:                  1.4
System identifier:        LAStools (c) by rapidlasso GmbH 
Generating software:      lasheight (190321) commercial 
File creation d/y:        267/2018
header size:              375 
Offset to point data:     2238 
Num. var. length record:  5 
Point data format:        6 
Point data record length: 36 
Num. of point records:    19517984 
Num. of points by return: 
Scale factor X Y Z:       0.01 0.01 0.01 
Offset X Y Z:             0 0 0 
min X Y Z:                7498400 5779500 -1.17 
max X Y Z:                7499200 5780000 25.94 
Variable length records: 
   Variable length record 1 of 5 
       Description:  GeoKeyDirectoryTag (mandatory) 
       Tags:
          Key 1024 tiff_tag_location 0 count 1 value offset 1 
          Key 1025 tiff_tag_location 0 count 1 value offset 2 
          Key 1026 tiff_tag_location 34737 count 13 value offset 0 
          Key 2048 tiff_tag_location 0 count 1 value offset 32767 
          Key 2049 tiff_tag_location 34737 count 7 value offset 26 
          Key 2050 tiff_tag_location 0 count 1 value offset 32767 
          Key 2051 tiff_tag_location 0 count 1 value offset 32767 
          Key 2052 tiff_tag_location 0 count 1 value offset 9001 
          Key 2054 tiff_tag_location 0 count 1 value offset 9102 
          Key 2056 tiff_tag_location 0 count 1 value offset 32767 
          Key 2057 tiff_tag_location 34736 count 1 value offset 0 
          Key 2059 tiff_tag_location 34736 count 1 value offset 1 
          Key 2060 tiff_tag_location 0 count 1 value offset 9102 
          Key 2061 tiff_tag_location 34736 count 1 value offset 2 
          Key 3072 tiff_tag_location 0 count 1 value offset 32767 
          Key 3073 tiff_tag_location 34737 count 13 value offset 13 
          Key 3074 tiff_tag_location 0 count 1 value offset 32767 
          Key 3075 tiff_tag_location 0 count 1 value offset 1 
          Key 3076 tiff_tag_location 0 count 1 value offset 9001 
          Key 3080 tiff_tag_location 34736 count 1 value offset 4 
          Key 3081 tiff_tag_location 34736 count 1 value offset 3 
          Key 3082 tiff_tag_location 34736 count 1 value offset 5 
          Key 3083 tiff_tag_location 34736 count 1 value offset 6 
          Key 3092 tiff_tag_location 34736 count 1 value offset 7 
          Key 4099 tiff_tag_location 0 count 1 value offset 9001 
   Variable length record 2 of 5 
       Description:  GeoDoubleParamsTag (optional) 
       data:                 6378137 298.2572 0 0 21 7500000 0 0.999923 
   Variable length record 3 of 5 
       Description:  GeoASCIIParamsTag (optional) 
       data:                 Poland2000s7|Poland2000s7|ETRS89| 
   Variable length record 4 of 5 
       Description:  OGC COORDINATE SYSTEM WKT 
   Variable length record 5 of 5 
       Description:  RIEGL Extra Bytes 
       Extra Bytes Description:
          Amplitude: Echo signal amplitude [dB]
          Reflectance: Echo signal reflectance [dB]
          Deviation: Pulse shape deviation

When I check Classification attribute: 

> max(las@data$Classification)
    [1] 5

I have also a TIF raster with treeIDs. I am using following algorithm to assign treeIDs to point cloud:

las_tree = lasmergespatial(las, tif_crop, "treeID")
treeID = las_tree@data[["treeID"]]
treeID = as.numeric(treeID)
las_tree = lasaddextrabytes(las_tree, x=treeID, name="treeID", desc="ID of a tree")

Now, las_tree has summary:

class        : LAS (LASFˇ v1.4)
point format : 6
memory       : 2.2 Gb 
extent       :7498400, 7499200, 5779500, 5780000 (xmin, xmax, ymin, ymax)
coord. ref.  : NA 
area         : 399973.7 units² (convex hull)
points       : 19517984 points
density      : 48.8 points/units²
names        : X Y Z gpstime Intensity ReturnNumber NumberOfReturns ScanDirectionFlag EdgeOfFlightline Classification ScannerChannel Synthetic_flag Keypoint_flag Withheld_flag Overlap_flag ScanAngle UserData PointSourceID Amplitude Reflectance Deviation treeID 
File signature:           LASFˇ 
File source ID:           4001 
Project ID - GUID:        df4425f5-d89d-437c-baa3-cd71726ed8c6 
Version:                  1.4
System identifier:        LAStools (c) by rapidlasso GmbH 
Generating software:      lasheight (190321) commercial 
File creation d/y:        267/2018
header size:              375 
Offset to point data:     2238 
Num. var. length record:  5 
Point data format:        6 
Point data record length: 36 
Num. of point records:    19517984 
Num. of points by return: 
Scale factor X Y Z:       0.01 0.01 0.01 
Offset X Y Z:             0 0 0 
min X Y Z:                7498400 5779500 -1.17 
max X Y Z:                7499200 5780000 25.94 
Variable length records: 
   Variable length record 1 of 5 
       Description:  GeoKeyDirectoryTag (mandatory) 
       Tags:
          Key 1024 tiff_tag_location 0 count 1 value offset 1 
          Key 1025 tiff_tag_location 0 count 1 value offset 2 
          Key 1026 tiff_tag_location 34737 count 13 value offset 0 
          Key 2048 tiff_tag_location 0 count 1 value offset 32767 
          Key 2049 tiff_tag_location 34737 count 7 value offset 26 
          Key 2050 tiff_tag_location 0 count 1 value offset 32767 
          Key 2051 tiff_tag_location 0 count 1 value offset 32767 
          Key 2052 tiff_tag_location 0 count 1 value offset 9001 
          Key 2054 tiff_tag_location 0 count 1 value offset 9102 
          Key 2056 tiff_tag_location 0 count 1 value offset 32767 
          Key 2057 tiff_tag_location 34736 count 1 value offset 0 
          Key 2059 tiff_tag_location 34736 count 1 value offset 1 
          Key 2060 tiff_tag_location 0 count 1 value offset 9102 
          Key 2061 tiff_tag_location 34736 count 1 value offset 2 
          Key 3072 tiff_tag_location 0 count 1 value offset 32767 
          Key 3073 tiff_tag_location 34737 count 13 value offset 13 
          Key 3074 tiff_tag_location 0 count 1 value offset 32767 
          Key 3075 tiff_tag_location 0 count 1 value offset 1 
          Key 3076 tiff_tag_location 0 count 1 value offset 9001 
          Key 3080 tiff_tag_location 34736 count 1 value offset 4 
          Key 3081 tiff_tag_location 34736 count 1 value offset 3 
          Key 3082 tiff_tag_location 34736 count 1 value offset 5 
          Key 3083 tiff_tag_location 34736 count 1 value offset 6 
          Key 3092 tiff_tag_location 34736 count 1 value offset 7 
          Key 4099 tiff_tag_location 0 count 1 value offset 9001 
   Variable length record 2 of 5 
       Description:  GeoDoubleParamsTag (optional) 
       data:                 6378137 298.2572 0 0 21 7500000 0 0.999923 
   Variable length record 3 of 5 
       Description:  GeoASCIIParamsTag (optional) 
       data:                 Poland2000s7|Poland2000s7|ETRS89| 
   Variable length record 4 of 5 
       Description:  OGC COORDINATE SYSTEM WKT 
   Variable length record 5 of 5 
       Description:  rlas extra bytes 
       Extra Bytes Description:
          Amplitude: Echo signal amplitude [dB]
          Reflectance: Echo signal reflectance [dB]
          Deviation: Pulse shape deviation
          treeID: ID of a tree

Checking Classification attribute again:

> max(las_tree@data$Classification)
[1] 5

When I write las_tree with writeLAS:

writeLAS(las_tree, savedFilename)

and read it again with: 

las_read <- readLAS(paste(path, savedFilename, sep="\\"))

seems like I lost Classification attribute values:

> max(las_read@data$Classification)
[1] 0

Summary of las_read:

class        : LAS (LASFˇ v1.4)
point format : 6
memory       : 2.2 Gb 
extent       :7498400, 7499200, 5779500, 5780000 (xmin, xmax, ymin, ymax)
coord. ref.  : NA 
area         : 399973.7 units² (convex hull)
points       : 19517984 points
density      : 48.8 points/units²
names        : X Y Z gpstime Intensity ReturnNumber NumberOfReturns ScanDirectionFlag EdgeOfFlightline Classification ScannerChannel Synthetic_flag Keypoint_flag Withheld_flag Overlap_flag ScanAngle UserData PointSourceID Amplitude Reflectance Deviation treeID 
File signature:           LASFˇ 
File source ID:           4001 
Project ID - GUID:        df4425f5-d89d-437c-baa3-cd71726ed8c6 
Version:                  1.4
System identifier:         
Generating software:      rlas R package 
File creation d/y:        0/2018
header size:              375 
Offset to point data:     2034 
Num. var. length record:  3 
Point data format:        6 
Point data record length: 44 
Num. of point records:    19517984 
Num. of points by return: 
Scale factor X Y Z:       0.01 0.01 0.01 
Offset X Y Z:             0 0 0 
min X Y Z:                7498400 5779500 -1.17 
max X Y Z:                7499200 5780000 25.94 
Variable length records: 
   Variable length record 1 of 3 
       Description:  by LAStools of rapidlasso GmbH 
       Tags:
          Key 3072 tiff_tag_location 0 count 1 value offset 32767 
   Variable length record 2 of 3 
       Description:  by LAStools of rapidlasso GmbH 
   Variable length record 3 of 3 
       Description:  by LAStools of rapidlasso GmbH 
       Extra Bytes Description:
          Amplitude: Echo signal amplitude [dB]
          Reflectance: Echo signal reflectance [dB]
          Deviation: Pulse shape deviation
          treeID: ID of a tree

Here's the full processing:

las = readLAS(filename_path, filter = "-keep_class 2 3 4 5")
tif_crop = raster::crop(tif, raster::extent(las)*1.1)
las_tree = lasmergespatial(las, tif_crop, "treeID")
treeID = las_tree@data[["treeID"]]
treeID = as.numeric(treeID)
las_tree = lasaddextrabytes(las_tree, x=treeID, name="treeID", desc="ID of a tree")
writeLAS(las_tree, savedFilename)
las_read <- readLAS(savedFilename)

Is that a lidR (rlas or liblas) error or I am doing something wrong?

Improve this question
5
  • Are you sure that the second summary of las_tree is the good one? treeID is missing into the header but it is present into las_read. I tried to reproduce your error without success. Are you sure you have an up-to-date version of rlas? LAS 1.4 is supported for not a long time
    – JRR
    Apr 15, 2019 at 16:04
  • rlas supports more properly LAS 1.4 PRF 6 since v1.3.0 (Release date: 2019-02-03)
    – JRR
    Apr 15, 2019 at 17:03
  • Thank you for your answer @JRR. I am using rlas 1.3.1 and lidR 2.0.2 I have edited the summary of las_tree. Nonetheless the classification is reset to 0 after saving. As an extra info I can say that CloudCompare doesnt see classification attribute at all on saved cloud. According to LasInfo (from Lastools) after saving min-max classification attribute values is 0. It used to be 2-5.
    – James Ch
    Apr 16, 2019 at 7:12
  • I reproduced. You found a bug. Their is something weird that happened with LAS 1.4 prf 6. Your code (or similar) works well with a LAS 1.3 file for example. It is not related to extabytes. Simply read/write a LAS 1.4 prf 6 file is enough to get Classification lost
    – JRR
    Apr 16, 2019 at 10:12
  • 1
    See issue github.com/Jean-Romain/rlas/issues/36
    – JRR
    Apr 16, 2019 at 10:24

1 Answer 1

Reset to default
4

The lidR package relies on the rlas package to read and write las file. The rlas package has a recent support of LAS 1.4 files (v1.3.0 release date: 2019-02-03). Moreover the point record formats >6 are a bit different than former point formats. Your code is correct and you actually found a bug in function write.las from rlas that occurs with point format 6 (at least). The bug you found has been fixed in rlas 1.3.2 (release date: 2019-04-26).

Otherwise your code is correct but it can be improved. The following is working and enought:

las_tree = merge_spatial(las, tif_crop, "treeID")
las_tree = add_lasattribute(las_tree, name="treeID", desc="ID of a tree")
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