Importing reference spectra for Raman Mapping

[dimaria789]

Hello
I am trying to import the csv file and cannot create a spectrum from this file. Maybe someone knows a trick.
Cheers
Thanks
Maria

[borondics]

Hi Maria,

Could you upload the file somewhere? We can have a look and hopefully help you out.

Ferenc

[dimaria789]

Thanks a lot!!
Of course, let me know where, here is the file.
fig 22-todorokte.csv

I digitalized this spectrum from a paper, and i have my own Raman mapping. The idea was to "teach" the QUASAR to make a minerals mapping.

[borondics]

Hello!

Try to use this workflow:
untitled.ows.zip

You can use either the File or the CSV File import widget but they need to be configured correctly.

Or:

I hope this helps.

[dimaria789]

Thanks! I did the same, and tried to transpose the column, but then the spectral data (the wavelength) is getting lost, you can see in the figure, the x-axis is from 1 to 200 instead of the wavelength (ca. 800 to 1800 cm-1). Thanks! Maria

[borondics]

I think you might need to click the "Remove redundant instance".

[dimaria789]

It is still not working, not giving the wavelength

[borondics]

You are right... Something seems funny here. @markotoplak, could you have a look?

[dimaria789]

Thanks!

[dimaria789]

Hi Ferenc
it is clicked and still I am getting
X axis 1 to 200, not the numeric data in the features, theres is a note: "Values are not unique.
To avoid multiple features with the same name, values
of 'Wave' have been augmented with indices."
Sorry, for the stupid problem.
Thanks
Maria

[dimaria789]

Hey Any advise, I still not getting the wave-numbers, but just counting on the X-axis Thanks a lot Maria Maria Dittrich, PhD Professor Earth Sciences Department University of Toronto 22 Ursula Franklin Street, M5S 3B1, Toronto Department of Physical and Environmental Sciences University of Toronto Scarborough 1265 Military Trail, M1C 1A4, Toronto ON, Canada

…

________________________________ From: borondics ***@***.***> Sent: June 14, 2024 10:45 AM To: Quasars/orange-spectroscopy ***@***.***> Cc: Maria Dittrich ***@***.***>; Author ***@***.***> Subject: Re: [Quasars/orange-spectroscopy] Importing reference spectra for Raman Mapping (Discussion #722) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> You are right... Something seems funny here. @markotoplak<https://github.com/markotoplak>, could you have a look? — Reply to this email directly, view it on GitHub<#722 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BHID5LXSJHBZOFN55G2CYGTZHL6XXAVCNFSM6AAAAABJGVU6KCVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TONZVGY4TG>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[markotoplak]

Maria, I tried the second option that @borondics showed above. I used the "File" for reading and then "Transpose", set to "From variable" to "Wave" and "Remove redundant instance" checked. Are you sure you did both? Or does what I am getting seem somewhat incorect?

If this does not help, can you show me a screenshot of related components? Here is mine.

[dimaria789]

Can you please check the spectra afterwards. This is what is not working. Thanks a lot!

[markotoplak]

Ok, now I finally understand the issue. Spectra can not understand your wavenumbers spectrum because some wavenumbers are repeating. Your data contains 734.2035432 and 738.4409664 twice. To work around it you could remove them with select columns after Transpose, like this. This is actually why the Transpose component has a warning triangle.

I know this is a lousy workaround but can not think of anything nicer.

Now that we understand why this is happening: is your data intentionally like this? If so, what do you aim to work on/display/analyze? I'd like to understand more about what you planned doing, because it seems that some components that could handle data like yours could be generally useful.

Furthermore, how did you imagine this spectrum (where some wavenumbers repeat) to be displayed? As an average on repeated wavenumbers? Or as multiple possibilities in plot, somehow marked by dots?

[dimaria789]

Mark, yes, I tried it, but when I go to the spectra, it does not show the wavelengths, but just count numbers 1-200, on the X-axis.
I followed your instructions, but now I am getting this

[markotoplak]

Could you show me what "File (1)" settings look like? It seems that "Intensity" role is set to "meta" in your case which it should no be. Can you try changing it (click on a cell and change them). Mine looks like this.

[dimaria789]

when I did CSV import:

I am getting 1-220 for the X-values,

and not the wavelengths:

[markotoplak]

Ok, now I finally understand the issue. Spectra can not understand your wavenumbers spectrum because some wavenumbers are repeating. Your data contains 734.2035432 and 738.4409664 twice. To work around it you could remove them with select columns after Transpose, like this. This is actually why the Transpose component has a warning triangle.

I know this is a lousy workaround but can not think of anything nicer.

Now that we understand why this is happening: is your data intentionally like this? If so, what do you aim to work on/display/analyze? I'd like to understand more about what you planned doing, because it seems that some components that could handle data like yours could be generally useful.

Furthermore, how did you imagine this spectrum (where some wavenumbers repeat) to be displayed? As an average on repeated wavenumbers? Or as multiple possibilities in plot, somehow marked by dots?

[dimaria789]

THANKS! It works now! Yes, I see the warning triangle. I ticked the remove the redundant instance. How did you find the doubles? No, BUT I digitalized it with origin, so my mistake! The idea is to "learn" the references spectra for the Raman mapping on Mn-Fe nodules from deep ocean, to see how Ni Co etc are incorporated. Maria Dittrich, PhD Professor Earth Sciences Department University of Toronto 22 Ursula Franklin Street, M5S 3B1, Toronto Department of Physical and Environmental Sciences University of Toronto Scarborough 1265 Military Trail, M1C 1A4, Toronto ON, Canada

…

________________________________ From: Marko Toplak ***@***.***> Sent: July 9, 2024 4:00 AM To: Quasars/orange-spectroscopy ***@***.***> Cc: Maria Dittrich ***@***.***>; Author ***@***.***> Subject: Re: [Quasars/orange-spectroscopy] Importing reference spectra for Raman Mapping (Discussion #722) Ok, now I finally understand the issue. Spectra can not understand your wavenumbers spectrum because some wavenumbers are repeating. Your data contains 734.2035432 and 738.4409664 twice. To work around it you could remove them with select columns after Transpose, like this. This is actually why the Transpose component has a warning triangle. image.png (view on web)<https://github.com/Quasars/orange-spectroscopy/assets/552182/1790783c-667f-432b-8657-b8809d8bfd61> I know this is a lousy workaround but can not think of anything nicer. Now that we understand why this is happening: is your data intentionally like this? If so, what do you aim to work on/display/analyze? I'd like to understand more about what you planned doing, because it seems that some components that could handle data like yours could be generally useful. Furthermore, how did you imagine this spectrum (where some wavenumbers repeat) to be displayed? As an average on repeated wavenumbers? Or as multiple possibilities in plot, somehow marked by dots? — Reply to this email directly, view it on GitHub<#722 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BHID5LV5U2VN7DTYL76SGBDZLOKA3AVCNFSM6AAAAABJGVU6KCVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TSOJVGU2TS>. You are receiving this because you authored the thread.Message ID: ***@***.***>