Specifically, our gridded FTIR-ATR runs have points with bad contacts, rendering those spectra useless (fringing effects, etc). We want to edit those few data points out but still produce a nice 3D map (albeit with a few holes). I've tried extracting a new 3D plot minus those blocks, but OPUS won't let me plot them except as columns or spots. Any suggestions? I have some experience with MATLAB, but I'm looking for a more elegant solution on OPUS. Thank you for your answers.
There is a possibility included in OPUS 7 3D. Just choose "Edit --> replace FPA oulying spectra" and enter the pixel number concerned. They are replaced with neighboring spectra, it usually works quite well. Alternatively, you could artificially generate "zero lines" as data point tables, convert them to OPUS format and use them to replace the problematic extracted spectra. Then you can assemble them to a new map file. I hope one of the approaches will help you.
Thank you, this should be very useful. We'll update with more specific instructions if we get it to work. Cheers!
Nathan, if I've got you right, you have undesirable points or fragments (spikes, fringes, etc.) in some of your SEPARATE spectral files? Then you assemble a MAP (3 D) file from a set of all SEPARATE files, and try to edit the 3D file?
There is another door to making fine-looking 3D files without artifacts in OPUS.
(1) Load a separate file and use "Straight Line Generation" function from "Manipulate" menu. Chose "Frequency Range" by your consideration and generate straight line between the two desirable abscissa points.
(2) Save the corrected file under appropriate name.
(3) Repeat the procedure with all problematic files.
(4) Reassemble the 3D file by using "Assemble GC File" or "Assemble Map File" routines from "Measure" menu. Certainly, you have to include the corrected files instead of the raw (problematic) ones into the whole set now.
Yet, there is a "Cut" function under the "Manipulate" menu in OPUS, which is very useful to remove the noisy margins in e.g. ATR files.
In any case, by my experience, it's more practical to edit separate files BEFORE assembling a 3D in OPUS, than to edit an assembled 3D product afterwards.
Hope it'll help. Good luck!
Alexander, Thank you. We collect ATR spectra in video assissted mode, so the spectra come together overlaid on the visible image. However, I have figured out how to extract all the spectra as if they had been collected separately (using the dialog box in the extract menu), and we have used this to extract small boxes of "good" data as you suggested (you can only extract a rectangle or square). We tried Julia's way, but have had some trouble (FPA is greyed out). Julia, are you working with FPA or ATR data? I wonder, we collect the data in Video Assisted Mode using OPUS 6.0 and then try to manipulate it using OPUS 7.0. I imagine this is causing some havoc as well.... Thank you both again for your useful suggestions. We'll update after we try again.
Hi everybody!
Could anyone please comment on realtive advantages and disadvantages of using the 3D features in OPUS vs. doing this in MATLAB.
Twenty years ago (when I was making these choices) I decided in favor of MATLAB, and I am still transforming my (time-resolved FTIR, i.e. 3D) OPUS data from Bruker IFS-66/s into MATLAB for all data manipulation.
Is OPUS nowadays so good that manipulating data there gives a advantage to using MATLAB?
Opus is not a good tool to manipulate datasest. I always export to matlab.
@ Nathan: I am using the FPA for chemical imaging of supersonic expansions, so I do not have any experience with ATR data. I have been working with the combination OPUS 6 + FPA as well, and all I can say about that is that there was more trouble than data, OPUS 7 is everything but perfect, but it's better.
@ Andrei: I am working with time-resolved as well as spatially resolved 3D data and I always export for the time-resolved ones. OPUS is only quite handy for fast generation of these nice colorful spacial maps.
As an extension to this, has anyone been able to export Grams 3Dmaps to MATLAB?
My GRAMS is so outdated that it cannot handle 3D data. Therefore, to work in 3D I export separate traces from GRAMS (as ASCII) into MatLab. BTW, how good/bad are the 3D features in GRAMS?
The resolution of the 3D maps of my version of Grams/32 (also old) is not great and there is no option on the software to plot 3D colour or mesh plots, only 2D plots. I was unable to export the map data collected with the Grams/32 on our Renishaw 1000 Raman spectrometer into a new version of Grams3D. So I really would like to export the map data into MATLAB. Do you save the spectra individually then build a matrix in MATLAB?
Copy it into e.g. COREL DRAW software (e.g. Corel Draw X4).
Degroup all elements and edit e.g.
Line thicknesses, spectra colours, offsets, fonts size etc.
Best regards,
Martin Müller
Ludovic, I assume that when you stated that you export dataset from opus to matlab, you talked about opus map file and not binary file. Could you describe how you managed to export dataset to matlab as I'm currently struggling to do so.
Many thanks in advance
Dear Guillaume,
I only just noticed your question. OPUS map files can be imported in CytoSpec and stored in a Matlab compatible data format. The demo version of CytoSpec is free of charge (limited functionality, runs for 90 days, registration will be required).
Best regards, -Peter
http://www.cytospec.com/ftir.php
- Badges
- Science topic
- Similar topics
- Correction