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@alexpok: nice samples, will take a look. Can you include the result of the original ZeroNoise with these files?

(I'm just curious to see how it works, since I couldn't run it)

In case of these examples it crashes on the last stage. I spent lot of time, push it to work - missing DLL in system, i have to set previous date on computer, compatibility mode with WinXP etc. But sometime (depends on files) it crashes on last stage - not enougth memory. Too much for me ( I have 64Gb (Win64)) - i decided to stop trying.

But i have cheked your patched Ufraw version ( i am not sure, that i know how to set all necessary options, but i dit what i can). The same problem - i put small jpeg files - how it looks to the same folder, and add the third file - you can see another (i think so) type of artifacts.

More interesting, i think - i try some (new for me) Photoshop workflow, emulating your program. I put processed cr2 files on separate layers, and try to use very nice option - layer blending with comdition. I simply take (not very precise) highlights from one image, and rest from brighter one. It works, but this procedure is time consuming and nonlinear by itself. Whats interesting - i have the same artifacts in the same place (on a cups), but have some walkaround - in Photoshop you can "split" the border of this algoritm, after this some of the pixels you take from first, some - from second, and certain critical amount on the border - mixed. This works. The result is not so bright and nice that in your program, but it works. Thats why i am sure, that particular this problem could be solved with moderate time.

[Addition of the next day].

I put the results (jpegs, but full res around 4 megs each) of both CeroNoice and my Photoshop method in the same subdir CeroNoice.Bad
The result of CeroNoice was processed 2 ways - by Adobe Camera Raw 8.3, and modified UFRAw. I should say, that result of UFraw looks much better - it doesnt have greenish color cast, and all artifacts much less prominent.
Now my image a little bit brighter - i modified method a little.

[endOfAddition]


PS.
The numbers (on the border) in this huge tif are pretty close, but i found this problem (much less prominent tho) even in "Good" situation.  May be performing all calculations in double (8 byte) could help. For example, with FFT i can perform multiplications of numbers with  millions decimal digits(nvidia CUDA) with double and only 10000 or so with float.  Even one wrong constant and conversion(8-4-8) can ruin all algorithm.

PPS. Thanks for your great work - its realy amaizing. I even did not believed my eyes trying RAW video and Dual ISO.

After having some trouble getting ZeroNoise working, I coded my own version of the algorithm (well, only the part I understood) and ran a little experiment to check whether you should really take as many brackets as you can, or whether you can get away with just 2 or 3 pictures spaced at 4 EV or more.

I've called my program CeroNoice, pronounced pretty much like ZeroNoise, with a Spanish "ce" ("hay que sacar la lengua").

I test this program lots of times, the image quality in result is amaizing, thanks for that a1ex - i also have a problems with original ZeroNoise.

I found some problems as well, i will try to describe them below, may be it helps to improve this wonderfull tool.

1. I decided to limit testing  by only 2 shots, 3EV difference. The reason - the quality already very good in case of no problems, in case of some problems additional files only makes it worse.

2. I made 2 sequences by 2 shots, run CeroNoice, run DNG_validate as described. The only difference between these sequences was one additional lamp turned on - it produces some highlights on scene. In good case (lamp off) i just process out.dng in Adobe Photoshop camera RAW 8.3 - i did not noticed any problems, just huge quality increase. In bad case (lamp on) green color cast appears on some objects - with highlights (best visible on white cups behind). Most important, that when checking resulting 32 bit tiff file  - it still exists and i can not imagine any transofmation, that can eliminate it - the area in wich it ocuurs has almost identical 
lighting, so you cant apply any curve (transformation).
  I think, that here some sort of rounding problem - this problem already exist in this huge 256 Mb tiff file.

I put a link to my Google  drive here  with these examples. I can say, that situation is quite repeatable in different conditions, in case of using 3 files blue color cast begins etc.
I have tried to make these examples illustrative, but may be made some mistake.

https://drive.google.com/folderview?id=0B72zfsjcoFZGanVIeVM5RDM4ZXc&usp=sharing

PS. I also did a comparison to the dual ISO in this case - also very good improvment over original version, but some noticable color artifacts (looks like chromatic aberrations, beter visible on a sauce bottle text on the left and power outlet on the wall). But very usable image in result. I also put it into the same directory.
WB - grey point below the name of coffemachine on the left. All image provided are Canon 5dIII .cr2