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How do I calculate a surface roughness index of multiple lidar point clouds with lidR rumple_index?

library(lidR)

files <- list.files(path= "/pathToFiles", pattern= "*.laz", full.names = TRUE, recursive = FALSE)

O = lapply(files, function(x) {
las = readLAS(x, select = "xyzc", filter = "-drop_z_below 0")
  chm = grid_canopy(las, 0.2, p2r())
  roughness <- rumple_index(chm)
  return(data.frame(file=x,roughness=roughness))
})
O = do.call(rbind,O)

However this code returns error:

    Error in C_rasterize(las, layout, subcircle, 1L) : 
  C++ unexpected internal error in 'rasterize': point out of raster.
In addition: Warning message:
In showSRID(SRS_string, format = "PROJ", multiline = "NO") : 

If I run the following code for a single file, it gives reasonable result.

las = readLAS("/input.laz", select = "xyzicnrRGB", filter = "keep_first -drop_z_below 0")
chm = grid_canopy(las, 0.5, p2r())
rumple_index(chm)

I found the file which was causing this error, below is a lasinfo report of that file.

lasinfo (190812) report for 'infile.las'
reporting all LAS header entries:
  file signature:             'LASF'
  file source ID:             0
  global_encoding:            0
  project ID GUID data 1-4:   00000000-0000-0000-0000-000000000000
  version major.minor:        1.4
  system identifier:          'LAStools (c) by rapidlasso GmbH'
  generating software:        'las2las (version 190623)'
  file creation day/year:     0/0
  header size:                375
  offset to point data:       469
  number var. length records: 1
  point data format:          6
  point data record length:   30
  number of point records:    0
  number of points by return: 0 0 0 0 0
  scale factor x y z:         0.00025 0.00025 0.00025
  offset x y z:               698292.56999999995 6104003.0700000003 0
  min x y z:                  698607.00800 6102989.34350 -0.03375
  max x y z:                  698698.55000 6103195.27825 19.08325
  start of waveform data packet record: 0
  start of first extended variable length record: 0
  number of extended_variable length records: 0
  extended number of point records: 363189
  extended number of points by return: 363189 0 0 0 0 0 0 0 0 0 0 0 0 0 0
variable length header record 1 of 1:
  reserved             0
  user ID              'LASF_Projection'
  record ID            34735
  length after header  40
  description          'by LAStools of rapidlasso GmbH'
    GeoKeyDirectoryTag version 1.1.0 number of keys 4
      key 1024 tiff_tag_location 0 count 1 value_offset 1 - GTModelTypeGeoKey: ModelTypeProjected
      key 3072 tiff_tag_location 0 count 1 value_offset 28355 - ProjectedCSTypeGeoKey: GDA94 / MGA 55S
      key 3076 tiff_tag_location 0 count 1 value_offset 9001 - ProjLinearUnitsGeoKey: Linear_Meter
      key 4099 tiff_tag_location 0 count 1 value_offset 9001 - VerticalUnitsGeoKey: Linear_Meter
reporting minimum and maximum for all LAS point record entries ...
  X             1257752    1623920
  Y            -4054906   -3231167
  Z                -135      76333
  intensity           0      42532
  return_number       1          1
  number_of_returns   1          1
  edge_of_flight_line 0          1
  scan_direction_flag 0          0
  classification      1          1
  scan_angle_rank     0          0
  user_data           0          0
  point_source_ID     0          0
  gps_time 164539.903446 168324.056522
  extended_return_number          1      1
  extended_number_of_returns      1      1
  extended_classification         1      1
  extended_scan_angle             0      0
  extended_scanner_channel        0      0
number of first returns:        363189
number of intermediate returns: 0
number of last returns:         363189
number of single returns:       363189
overview over extended number of returns of given pulse: 363189 0 0 0 0 0 0 0 0 0 0 0 0 0 0
histogram of classification of points:
          363189  unclassified (1)

I am using lidR_3.0.1 raster_3.1-5 sp_1.4-2

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  • 1
    unexpected internal error. This message speaks for itself. One of your point-clouds fall into an unexpected behavior partially handled internally. Please find which one, make a reproducible example and report this issue. Has an hint to make a minimal reproducible example: it comes from p2r() and is not related to rumple_index(). Also please mention the version and ensure you run a recent version of the package. This bug has already been fixed. It might be a new one but maybe not.
    – JRR
    Commented Oct 30, 2019 at 12:43
  • Thanks @JRR, yes one of the files was misbehaving. Interestingly, I couldn't file which one. I divided files into few folders and tried to run the code for each folder separately. Only one folder returned the same error. I tried to run the code for each file one by one in that folder and got the result without any problem.
    – Sher
    Commented Nov 1, 2019 at 6:23
  • 1
    Add print(x) in your function and you will find the file that fails
    – JRR
    Commented Nov 1, 2019 at 10:19
  • @JRR, just letting you know that print(x) didn't find the file which was failing. Thanks for your help.
    – Sher
    Commented Nov 6, 2019 at 0:18
  • @JRR. I found a file which was causing above mentioned error and added lasinfo report of that file. Could you please have a look and let me know if something is wrong with it? I couldn't see any problem.
    – Sher
    Commented Jun 25, 2020 at 5:53

1 Answer 1

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In your first example, when calculating roughness of multiple laz files, you specify a resolution of 0.2 chm = grid_canopy(las, 0.2, p2r()). In the second example, you specify a resolution of 0.5 chm = grid_canopy(las, 0.5, p2r()).

I have found I also get this error:

Error in C_rasterize(las, layout, subcircle, 1L) : C++ unexpected internal error in 'rasterize': point out of raster.

when using a resolution of 0.2, but it works when I set a lower res (i.e., 0.25, 0.5, etc.)

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