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Support new header entry for OPUS file posted here: https://github.com/wincowgerDEV/OpenSpecy-package/issues/118 #95
Comments
devtools::load_all()
#> ℹ Loading opusreader2
file <- system.file("extdata", "new_data", "OpenSpecy-package_issue118.0",
package = "opusreader2"
)
data <- read_opus(dsn = file)
#> Error: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b15-c40-t0-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots. Created on 2023-11-07 with reprex v2.0.2 |
The single channels work so far, for the remaining blocks we need screenshots to try-error parsing settings. {opusreader2} v0.6.0: see also https://github.com/spectral-cockpit/opusreader2/blob/main/NEWS.md library("opusreader2")
file <- "inst/extdata/new_data/issue118_OpenSpecy-package.0"
data <- read_opus(dsn = file)
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b15-c40-t0-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b7-c132-t0-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b23-c132-t0-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b7-c4-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b23-c4-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b7-c132-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b23-c132-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b11-c132-t0-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b27-c132-t0-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b11-c4-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b27-c4-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b11-c132-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b27-c132-t1-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b31-c40-t0-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning: Unknown header entry.
#> The following 'composite key' is not yet mapped in the {opusreader2} key-value map of the header:
#> * "b0-c0-t8-a64"
#> We encourage your contribution to feature this new OPUS block by opening a new issue on
#> https://github.com/spectral-cockpit/opusreader2/issues
#> Please
#> 1. report reproducibly, using short code with {opusreader2}
#> (recommended: https://reprex.tidyverse.org)
#> 2. describe briefly
#> a) Bruker instrument used
#> b) equipment
#> c) measurement mode and spectral blocks saved (OPUS settings)
#> d) OPUS software version
#> e) your general workflow for spectroscopic diagnostics
#> 3. provide an example OPUS binary file uploaded for public access
#> on GitHub (best in issue)
#> 4. to facilitate widespread support of Bruker devices in open source
#> based infrastructure, show the data blocks as print screens in the
#> Bruker OPUS software (right-click in Viewer). Please upload the
#> contents of all OPUS blocks in individual screenshots.
#> Warning in get_meta_utc_datetime(timestamp): NAs introduced by coercion
names(data[[1]])
#> [1] "basic_metadata" "sc_ref_data_param" "sc_ref"
#> [4] "optics" "sample" "instrument"
#> [7] "history" "unknown"
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 |
I am able to read this file from my python package: https://github.com/joshduran/brukeropus Here is the file directory (header):
You can see there are several data blocks with unknown labels, but they parse as data arrays (or parameters where labeled). I can look into trying to determine descriptive labels for these unknown type codes (33, 65, 97) so they can be presented to the user more cleanly. If you aren't doing this already, you can see I break the block type integer into 6 parts (bit shifting). This is the key to broadly classifying these blocks (i.e. reliably determine if parameter block, data block, 3D data block, etc... here is the full output if it helps:
|
refers to wincowgerDEV/OpenSpecy-package#118
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