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Amusing. I'm a little disturbed by the first one (going to two destinations, depending on variations in the code read) because I can't think of many uses for it that aren't malware-ish.
As for the logo, there are only two methods: to use proprietary generators that will work around a "dead zone" of defined size and shape — meaning, almost without exception, you'll pay for the privilege and it may be tied to a metered/redirected link on top of that.
It is fairly simple, though, to simply lay in a logo of reasonable size and mask over part of the code; with the error correction turned up, you can blank over a good quarter of code and still have it read reliably. (Sub-trick: make sure you cleanly truncate and block the grid, rather than leaving partial squares of either color.) InDesign is limited to one error correction level (M, 15% correction), so if you can't get it to work in here, you'll have to use a code generator that can handle the Q or H levels. It's the error correction that compensates for the missing pixels, so higher is better.
Like this, no fancy color-masking needed, just a bit of experimentation and then some cleanup —
Someday someone will release a reliable, full-featured QR code generator that handles the full spectrum of options, allows for interactive logo placement and isn't simply a come-on/hook/subterfuge for malware or pay-me. 🙂
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Knowing how text is stored:
https://en.wikipedia.org/wiki/QR_code#Message_placement
It should be pretty easy to "avoid" places covered by image...
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There are probably any number of ways to optimize logo placement, but the whole point of error correction is that some XX% of the code will be unreadable or misread and the content can be recreated from the redundant encoding.
I'm not sure any human-managed tricks will work; the encoding algorithms are phenomenally complex. (Look up the defining standard ISO/IEC 18004:2015 and bring some aspirin. Here's a link to a PDF. There is a newer version, :2024, but it seems to be pay-access only so far.)
From my experience, you can plop a logo onto a generated code with these steps —
You'll probably find that most readers (use at least two, if you have them handy) will read the code in a moment or two, or even with no delay, almost anywhere you put the blocking square.
If the logo is irregular (e.g. a bird with spread wings, an asymmetrical text logo, etc.) you can restore square areas of pixels around it, both for esthetics and to increase readability.
And, if you use a tool other than ID to generate the (final) QR code, crank up the error correction factor to the third or fourth level, and reads will be all but unimpaired.
To circle back around, it's possible some advanced analysis would show better and worse places to put the logo for readability, but I'd have to see hard results to be convinced such effort pays off on top of the above "try and try again" methods.