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AFF SEQ Files #22

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mkostrun opened this issue Mar 17, 2023 · 11 comments
Open

AFF SEQ Files #22

mkostrun opened this issue Mar 17, 2023 · 11 comments

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@mkostrun
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This is more of a comment than issue:

I have an ancient FLIR SC6000 camera which came with even more ancient software for camera control/data acquisition called ExaminIR v. 1.20, so called, Basic version (as opposed to Pro and Max).

The basic version records thermal movies as files with an extension .SEQ. Their header suggests it is an Agema File Format (AFF) for sequence of thermal images. The exiftool cannot read these files (reviewing its source code suggests only the files with header FFF can be read). Flir software tools cannot read the format either (tested with ResearchIR, and so forth).
I was wondering if you had insights into AFF beyond what exiftool does and does not provide. Do you have a copy of later version of Examin IR, or Pro or Max?

Currently, for me the only way to get the frames out without relying on a supply of graduate students or interns, is to do some desktop programming, and have that program move the cursor around to extract the images into csv files, but this takes 20seconds/frame.

Thanks,

@gtatters
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what FLIR does from software to software, camera to camera is always a mystery (purposely no doubt). maybe send me a sample file since I don't know what your question really is. As you can tell from this package, we make use of exiftool's extraction capacity.

@mkostrun
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mkostrun commented Mar 17, 2023 via email

@gtatters
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Splitting the files should still be possible. Admittedly, this R package isn't the best for working with videos since R isn't a fast environment to work. You could explore some bash/terminal code I've shared here: https://github.com/gtatters/ThermimageBash

I know this code works on old .SEQ files collected with Thermocam Researcher Pro as far back as 2008 when I first started collecting. It also works on .SEQ or .FCF files collected with ExaminIR.

But Thermimage mostly converts the files into their raw data, and then those raw files can be imported into ImageJ and you could use ThermimageJ (https://github.com/gtatters/ThermimageJ) to convert the raw data into temperature. These files would be smaller than working with .csv temperature files anyway.

If you have a small file you want me to test things out with to verify the code can operate on it, please feel free to share via wetransfer.com. My email can be found on my lab website: https://tattersalllab.com/contact-information/

@mkostrun
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mkostrun commented Mar 18, 2023 via email

@gtatters
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my perl script (split.pl) can recognise some headers and that's what I will try with a sample file. The default one I'd first look for is "\x46\x46\x46\x00" but can try some others, simply to get and .fff file.

@gtatters
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The more up to date one is on ThermimageJ: https://github.com/gtatters/ThermImageJ/blob/master/scripts/split.pl

@mkostrun
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mkostrun commented Mar 18, 2023 via email

@gtatters
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Not sure there will be any info on the conversion from 16bit to float within the file, but what could be stored within the info prior to the pixel start will be calibration constants for the conversion. Exiftool might be able to extract them for you.

https://exiftool.org/TagNames/FLIR.html

EEVBlog have a huge forum discussing how to convert FFF files into temperature.

And Walter Minkina's book discusses the algorithm to convert the raw value into temperature.
Minkina, W. and Dudzik, S. 2009. Infrared Thermography: Errors and Uncertainties. Wiley Press, 192 pp.

the conversion formula is also contained within the raw2temp() function in the Thermimage package, but requires that you have the calibration coefficients (exiftool refers to them as Planck coefficients in reference to the formula used).

maybe try running:

exiftool yourfilename.seq

and share the output here?

@mkostrun
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mkostrun commented Mar 19, 2023 via email

@gtatters
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yes, a quadratic describing the relationship between the raw data and temperature would work. It's one of the solutions I have in my imageJ code.

@turgut-aydemir
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Hi, i have a huge .seq file (21GB) and i need to read temperature values for each frame of it. how can i do it?

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