Capture and parse output of lascheck from lidR

Question

To aid in quality control of a set of LAS files, I would like to write out all errors/warnings from lascheck(), for each LAS file (i.e. so not the LAScatalog implementation of lascheck(()). I'm looking for any tips to extract lascheck() warnings while looping through the entire list.

Answer 1

Anwser for lidR version 2.x.y

lascheck() does not return anything. It only prints. It might be seen as a design mistake and it is fair to think that. However we can find a workaround by capturing the standard output. lascheck() prefixes what is considered as a warning with the symbol ⚠ (\u26A0) and what is considered an error with ✗ (\u2717). You can grep these symbols.

library(lidR)
LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
las = readLAS(LASfile)

las$ReturnNumber[1] <- 0L # Introduce warnings
las@header@PHB$`Point Data Format ID` <- 12L # Introduce errors.

check = capture.output(lascheck(las))

warn_pos = grep("\u26A0", check)
warns = trimws(check[warn_pos])
warns
#> [1] "⚠ Invalid data: 1 points with a return number equal to 0 found."                                     
#> [2] "⚠ 'PointSourceID' attribute is not populated."                                                       
#> [3] "⚠ 'EdgeOfFlightline' attribute is not populated."                                                    
#> [4] "⚠ Invalid file: the header states the file contains 55756 returns numbered '1' but 55755 were found."

err_pos = grep("\u2717", check)
errs = trimws(check[err_pos])
errs
#> [1] "✗ Invalid data: ReturnNumber is not an unsigned integer"                                                     
#> [2] "✗ Invalid header: The point data format 12 is not part of the LAS specifications."                           
#> [3] "✗ Invalid file: the data contains a 'gpstime' attribute but point data format is not set to 1, 3, 6, 7 or 8."

^{Created on 2020-02-24 by the reprex package (v0.3.0)}

Answer for lidR version 3+ (to be released)

las_check() has an option print = FALSE

las_check(las, FALSE)
#> $warnings
#> [1] "Invalid data: 1 points with a return number equal to 0 found."                                     
#> [2] "'PointSourceID' attribute is not populated."                                                       
#> [3] "'EdgeOfFlightline' attribute is not populated."                                                    
#> [4] "Invalid file: the header states the file contains 55756 returns numbered '1' but 55755 were found."
#> 
#> $errors
#> [1] "Invalid data: ReturnNumber is not an unsigned integer"                                                     
#> [2] "Invalid header: The point data format 12 is not part of the LAS specifications."                           
#> [3] "Invalid file: the data contains a 'gpstime' attribute but point data format is not set to 1, 3, 6, 7 or 8."