After a good few clear nights for the first time in forever and a few recent equipment upgrades, I am hoping I have some decent data to process! I am going to finally try the pixinsight trial so want to hit the ground running and have been searching the forums and watching the Adam Block videos on Youtube.
I can answer this better when I get home from work and look at my directory structure.
Basically I would say yes that level of organisation is fine but you need to add an underscore after the keyword you want to use as PI uses the underscore as a marker to look for the keywords.
I would never delete any original images, including the flats and darks, although if you are perfectly happy the master dark and master flat are both good then you could just keep the masters.
Problem is you can't really just take flats again and be 100% sure they are correct for the nights imaging if done months later, or even days later if anything in the image train has moved.
External hard drives 1Tb and bigger are not expensive now, SSD can be but even 1TB SSD not too expensive, and I would recommend getting one and do not delete anything until you have have final images you are happy with. Even then it can be good to save what you can as months, years later you often want to reprocess as you either get better at it or new tools become available and it is very frustrating when calibration files are lost.
Always best to have any data you are processing on the main harddrive as accessing a slower external drive can slow things down a lot and get frustrating, but they are great for long term storage or even backing up data from other drives in case one goes down you do not want that to be the only source of your data.
Create a darks library for all exposure times you think you will use so that you end up with a library of dark masters. this way you then only have to have the masters on your main pc rather than all the dark frames.
Same goes for a bias if using one.
Update this every 12 months or so.
You can use WBPP to do this and run it just without any light images or flats.
Copy all the lights and flats from your session, or sessions, you want to process from external drive to PC if there is room on PC.
If not you can process directly from the external drive but it can take considerably longer, i would experiment and see if the time difference is extreme, if not too much more maybe makes sense to process directly from the external drive rather than having copies on main pc drive.
Carry on with the post processing saving the Pixinsight project ro PC or the external hard drive, your choice depending on how the emory is going on the PC so you can retrieve your project later to carry on processing or if you have an unexpected shut down of your PC at any time.
One thing i have done on my laptop (which is quite old and not an all singing and dancing model) is that it has a CD / DVD drive in what is called a bay. I never really used it anymore as all software comes on line these days. You can but a bay that holds a 2nd hard drive and replace the cd drive with the 2nd hard drive. Cost me about 80 including the SSD hard drive and bay for an extra 1TB of fast SSD memory, so not sure if this is something you could consider.
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