Error reading an Opus file

[zecojls]

Hi, I'm trying to read an Opus file from a collaborator, and the following error is raised:
"Error in ds_param[[1]] : subscript out of bounds"

Reproducible code:
test <- read_opus_single(dsn = "RT_01_1_23-02-21_13-23-54.0")

The binary Opus file was sent by email to help with debugging. The data comes from a Bruker 2023 Alpha II.

I'm also attaching the screenshots of the file blocks.

Thanks

[zecojls]

[philipp-baumann]

Hi, I'm trying to read an Opus file from a collaborator, and the following error is raised: "Error in ds_param[[1]] : subscript out of bounds"

Reproducible code: test <- read_opus_single(dsn = "RT_01_1_23-02-21_13-23-54.0")

The binary Opus file was sent by email to help with debugging. The data comes from a Bruker 2023 Alpha II.

I'm also attaching the screenshots of the file blocks.

Thanks

Thanks @zecojls for the screenshots and the issue, @ThomasKnecht and me will investigate and hopefully fix the coming WE. Will keep you up to date. Kind regards, Philipp

[philipp-baumann]

Hi @zecojls we were able to fix it :-) More infos about v0.6.0 that supports it are here https://github.com/spectral-cockpit/opusreader2/blob/main/NEWS.md

library("opusreader2")
file <- "inst/extdata/new_data/issue94_RT_01_1_23-02-21_13-23-54.0"
data <- read_opus(dsn = file)
names(data[[1]])
#>  [1] "basic_metadata"             "ab_no_atm_comp_data_param" 
#>  [3] "ab_no_atm_comp"             "sc_sample_data_param"      
#>  [5] "sc_sample"                  "sc_ref_data_param"         
#>  [7] "sc_ref"                     "optics"                    
#>  [9] "optics_ref"                 "acquisition_ref"           
#> [11] "fourier_transformation_ref" "fourier_transformation"    
#> [13] "sample"                     "acquisition"               
#> [15] "instrument_ref"             "instrument"                
#> [17] "history"
sessionInfo()
#> R version 4.1.3 (2022-03-10)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=de_CH.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=de_CH.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=de_CH.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] opusreader2_0.6.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.33     withr_2.5.0       R.methodsS3_1.8.2 lifecycle_1.0.3  
#>  [5] magrittr_2.0.3    reprex_2.0.2      evaluate_0.22     rlang_1.1.1      
#>  [9] cli_3.6.1         rstudioapi_0.15.0 fs_1.6.3          R.utils_2.12.2   
#> [13] R.oo_1.25.0       vctrs_0.6.3       styler_1.10.2     rmarkdown_2.24   
#> [17] tools_4.1.3       R.cache_0.16.0    glue_1.6.2        purrr_1.0.2      
#> [21] xfun_0.40         yaml_2.3.7        fastmap_1.1.1     compiler_4.1.3   
#> [25] htmltools_0.5.6.1 knitr_1.43

^{Created on 2023-11-12 with reprex v2.0.2}

You can just do an remotes::install_github("spectral-cockpit/opusreader2") to get the newest version.
Once you confirm we can close the issue here.

[zecojls]

Great! Thank you guys. Just to confirm with a quick silly question, what is the equivalent R list name to the Opus AB block?

[philipp-baumann]

ab_no_atm_comp -> see help https://spectral-cockpit.github.io/opusreader2/reference/read_opus.html . Here no CO2/H2O compensation has been done. Our reader can retrieve 2 AB blocks if atmospheric compensation was set in OPUS, meaning we can get both raw apparent abs and the atmospherically correctet apparent abs (propr. OPUS macro). In such a case, although both are present in the file, OPUS software would only show the final compensated spectra in the viewer, which isn't so clever for scalable spectroscopy workflows. Hence the special name ;)

[zecojls]

Perfect, thank you. I think in the previous versions the description was not that clear but I'm glad to see you guys improved it a lot. I've been using the reflectance data and transforming it to apparent absorbance with log10(1/R) rather than natural log. Not sure if makes sense to properly document it as log10 for those not familiar with these transformations...

[philipp-baumann]

Perfect, thank you. I think in the previous versions the description was not that clear but I'm glad to see you guys improved it a lot. I've been using the reflectance data and transforming it to apparent absorbance with log10(1/R) rather than natural log. Not sure if makes sense to properly document it as log10 for those not familiar with these transformations...

ok, great. Fair point, log10 would be good to name explicitly to not confuse with ln.

[philipp-baumann]

just fixed to log10(...) 850fa73