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I'm not 100% certain, but on ALIENS for example, it looks to me there are zooms added to the different cropping (like when they first see a victim and burn the Alien coming out of her). So that means it's not just a case of overlaying better resolution transfers, you also have to take into account Cameron added zooms to the Pan & Scan versions, and actually, I do remember him saying he would improve the film that way when doing the P&S master.
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I've spent probably about 3-4 hours now testing, retesting, trying every possible setting.. I cannot get 2 identical scenes (same rez, similar color grading, same fps, etc.) to overlay correctly in Auto Overlay avisynth. Is it because one is PAL widescreen and the other is PAL fullscreen? I want to overlay the higher quality widescreen footage on top of the lower quality fullscreen, so it becomes like an "open matte". Would it help if I artificially forced one or the other's aspect ratio? I also cropped the widescreen one.. didn't make any difference. Res of both are 720x576 (widescreen one gets down to 544 if I crop). Here's my script, which is prob full of mistakes:
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widescreen=directshowsource("V:\PAL SCENE 16x9-from premiere.mov")
openmatte=directshowsource("V:\PAL SCENE Full Frame-from premiere.mov")
OverlayConfig(aspectRatio1=1.78, subpixel=3)
OverlayEngine(openmatte, widescreen, editor=true)
#ComplexityOverlay(widescreen, openmatte)
OverlayRender(openmatte, widescreen, colorAdjust=1, mode=3, gradient=20)
#OverlayCompare(widescreen, openmatte)
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Welcome to my world. Same issues for me no matter the settings I can never get alignment.