If you want to batch process, the only solution I know is to process your raw files first to split them into R, B, and B fits files. You would then load the fits files as three separate stacks in AstroImageJ.
The best tool I've seen for doing this with Canon files is the Python routine "cr2fits.py". It is available here:
https://github.com/eaydin/cr2fitsIt depends only on widely available Python libraries, and will produce a fits file in a selected filter. You would have to set it up in a repetitive script to do this for all files in a directory, and for each of the R,G, and B bands you wanted to extract. However, it would be hands-off once started.
If you have only a few files and want to interact with them, then you can use the ij-dcraw plugin or dcraw itself to produce a 16--bit tiff color image from the raw file. The plug-in is here:
http://ij-plugins.sourceforge.net/plugins/dcraw/You copy it into the plugins directory of your AstroImageJ installation. It also needs a dcraw binary specific to your operating system that must be in plugins/dcraw . In Linux, if you have dcraw already just make this directory under plugins and then cd dcraw, "ln -s /usr/bin/dcraw dcraw" so that AstroImageJ will find it. (Or put another copy of it there).
when you open the plugin it will prompt for a file, offer some options, and then convert and load the 3 filters as separate images in a color stack. You would have to separate them from the stack, and reorganize to do the photometry on a new stack for each filter. I do not know how to automate this process, but probably with an IJ macro you could do the whole task inside AstroImageJ.
I tried both approaches with some sample RAW Canon (non-astronomical) images from the web and this seems to give the results needed to do photometry on DSLR color images. I don't have any astronomical Canon images to try though.
If you have dcraw itself, you can read the raw file and convert it to a 16-bit linear tiff, which can then be loaded directly into AstroImageJ. The appropriate dcraw command is
dcraw -4 -T file
and the output will be a file with a tiff extension. You can then load that tiff image into AstroImageJ and it will appear as a 16-bit color stack.
With the "-4 -T" command line option, dcraw will make a linear image file without trying to make the corrections that may be in the raw file header. dcraw will process in batch, and you can use a wildcard for the "file" to have all of them done at once and returned as separate tiff files.
This does not seem to be particularly useful for AIJ because when you load a stack of 16-bit color tiffs they separate sequentially in the same stack -- image1-R, image2-G, image1-B, image2-R and so on.
It seems if you have many files, the simplest approach would be to do the separation into fits files for each color first and then load those into AIJ for processing.
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