spectral-cockpit/opusreader2

Support OPUS files with normalization in AB block

Closed this issue · 20 comments

Debora6991 commented

Hi!
I obtain this error when I try to read my OPUS files both with the single and multiple read approach,

image

image
I am using an old TENSOR 27 FTIR spectrometer, equipped with HTS-XT accessory (OPUS 6.5)
What should I do?

philipp-baumann commented

Hi @Debora6991 , could you upload your example OPUS file, e.g. "A1.1.0"

Debora6991 commented
philipp-baumann commented

Hi Debora, which email did you send it to?

Debora6991 commented

I answered directly by email because here the format file is not allowed. this is the e-mail address that appears
AMCFBHYD6V27XJ5QHK5ND2WCEVWOREVBNHHGCQG6QI@reply.github.com.

Is this right? where should I attach the .0 OPUS file?

philipp-baumann commented

gosh stupid github, it used to support random binary files ;-) can you please send an email to spectral-cockpit at protonmail dot com ? thanks

Debora6991 commented

e-mail sent.
Thankyou!

philipp-baumann commented

got it! I'll give it a try this week. Could you please add screenshots of the OPUS software view (as described in informative message?) thanks (ATM do not have a direct access to the software)

Debora6991 commented
philipp-baumann commented

would be nice to have all spectral blocks screenshotted (right click on file...) :-) => here is a brief example: #58
easiest would be just pasting screenshot images here.

philipp-baumann commented

I want to just make sure everything we parse is double-checked on the OPUS side.

Debora6991 commented
philipp-baumann commented

Hi Debora, I do not see any images in your response above. Can you send them to me via mail?

philipp-baumann commented

alternatively, can you give me a brief info here what all the block names are? I need an extra block type if you want your setting to be supported.

philipp-baumann commented

@Debora6991 I think you did an email, but I did not receive, because it went to some GitHub address. If you want, I can post screenshots the file settings here? Respectively, I am in Zurich today early evening and could have access to OPUS software in a lab at ETH Zürich.

Debora6991 commented
  • 🎉1
philipp-baumann commented

I sent the mail again (spectral-cockpit protonmail....), did it work?
…
On Thu, Mar 23, 2023, 11:35 Philipp Baumann @.> wrote: @Debora6991 https://github.com/Debora6991 I think you did an email, but I did not receive, because it went to some GitHub address. If you want, I can post screenshots the file settings here? — Reply to this email directly, view it on GitHub <#81 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMCFBHY3JOTBO5KD24A3BMDW5QRQHANCNFSM6AAAAAAWAYQ56U . You are receiving this because you were mentioned.Message ID: @.>

awesome, it got it. Will keep you posted.

Debora6991 commented
philipp-baumann commented

just a short info to let you know. I am currently underway with my bike travelling. Eventually I have time I might push the necessary changes, but it can also be June until I am able to do so. Cheers

philipp-baumann commented

Hi @Debora6991 finally there is a fix for your issue :-)
With version 0.6.1 (see ) it should now work (see here https://github.com/spectral-cockpit/opusreader2/blob/main/NEWS.md )

library("opusreader2")
file <- "inst/extdata/new_data/issue81_A1.1.0"
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"                "fourier_transformation"   
#> [11] "sample"                    "acquisition"              
#> [13] "instrument_ref"            "instrument"               
#> [15] "lab_and_process_param_raw" "info_block"               
#> [17] "quality_test_report"       "history"
data[[1]]$quality_test_report
#> $block_type
#> [1] 15
#> 
#> $channel_type
#> [1] 16
#> 
#> $text_type
#> [1] 96
#> 
#> $additional_type
#> [1] 0
#> 
#> $offset
#> [1] 28440
#> 
#> $next_offset
#> [1] 31200
#> 
#> $chunk_size
#> [1] 2760
#> 
#> $block_type_name
#> [1] "quality_test_report"
#> 
#> $parameters
#> $parameters$BID
#> $parameters$BID$parameter_name
#> [1] "BID"
#> 
#> $parameters$BID$parameter_name_long
#> NULL
#> 
#> $parameters$BID$parameter_value
#> [1] 6295567
#> 
#> $parameters$BID$parameter_type
#> [1] "int"
#> 
#> 
#> $parameters$NRP
#> $parameters$NRP$parameter_name
#> [1] "NRP"
#> 
#> $parameters$NRP$parameter_name_long
#> NULL
#> 
#> $parameters$NRP$parameter_value
#> [1] 1
#> 
#> $parameters$NRP$parameter_type
#> [1] "int"
#> 
#> 
#> $parameters$SIZ
#> $parameters$SIZ$parameter_name
#> [1] "SIZ"
#> 
#> $parameters$SIZ$parameter_name_long
#> NULL
#> 
#> $parameters$SIZ$parameter_value
#> [1] 124
#> 
#> $parameters$SIZ$parameter_type
#> [1] "int"
#> 
#> 
#> $parameters$TIT
#> $parameters$TIT$parameter_name
#> [1] "TIT"
#> 
#> $parameters$TIT$parameter_name_long
#> NULL
#> 
#> $parameters$TIT$parameter_value
#> [1] "Quality Test Report"
#> 
#> $parameters$TIT$parameter_type
#> [1] "str"
#> 
#> 
#> $parameters$E00
#> $parameters$E00$parameter_name
#> [1] "E00"
#> 
#> $parameters$E00$parameter_name_long
#> NULL
#> 
#> $parameters$E00$parameter_value
#> [1] "Quality Test Report"
#> 
#> $parameters$E00$parameter_type
#> [1] "str"
#> 
#> 
#> $parameters$F00
#> $parameters$F00$parameter_name
#> [1] "F00"
#> 
#> $parameters$F00$parameter_name_long
#> NULL
#> 
#> $parameters$F00$parameter_value
#> [1] 2012
#> 
#> $parameters$F00$parameter_type
#> [1] "int"
#> 
#> 
#> $parameters$Z00
#> $parameters$Z00$parameter_name
#> [1] "Z00"
#> 
#> $parameters$Z00$parameter_name_long
#> NULL
#> 
#> $parameters$Z00$parameter_value
#> [1] 748
#> 
#> $parameters$Z00$parameter_type
#> [1] "int"
#> 
#> 
#> 
#> attr(,"class")
#> [1] "parameter"

Created on 2023-11-12 with reprex v2.0.2

philipp-baumann commented

It was a new parameter block, calling "quality_test_report", which probably exists due to a OPUS macro used.