Weird stacking problems with Zerene Stacker

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Macro_Cosmos
Posts: 681
Joined: Mon Jan 15, 2018 9:23 pm
Location: Sydney

Weird stacking problems with Zerene Stacker

Post by Macro_Cosmos »

I've been using the software for quite some time. I previously found that Zerene Stacker does not handle LCD/OLED screens quite well. The software gets confused and does some very weird stuff. Disabling alignment fixes it.

I've identified another weird, extremely specific stacking issue today, and I don't know if there's a way around it or not. I think there's a method but it will be too troublesome and inconvenient to execute.

When the scene is completely green-ish, the software simply confuses itself and produce extremely washed out and displeasing results.

The target is a Papilio Palinurus Daedalus butterfly. I chose two sections, one entirely green, the other has some patterns and darker scales (the bones of the wings? I don't know the technical term)

Camera used, objective, and lighting are all controlled. Nothing environmental is changed. It's easier to explain all this with sample photos.

Here is the scene with the "interspace lining" visible:
Image
Full resolution: https://farm5.staticflickr.com/4888/459 ... bb21_o.jpg
Nothing weird or worrying here.

Here's "all green":
I used Dmap after aborting the Pmax stack since it produced weird results. Dmap is no different.
Image
Full resolution: https://farm5.staticflickr.com/4889/466 ... 8222_o.jpg

Lots of weirdness going on here, the shadow region is smudged, there's haloing and the image is greyish, lacks any depth or dimension. I can even see bits of blue for some reason. This is actually after I edited the photo. The unedited version looks far worse. Here's a 1:1 screenshot.
Image

For contrast, I sent shrunken jpeg photos to a friend. He used his own software and ran a stack:
Image
Full resolution: https://farm5.staticflickr.com/4854/459 ... 3667_o.jpg
It is shrunken, sending over 50GB of files on Aussie interweb speed isn't viable. It will be faster to just mail him an SD card. There's however none of the weirdness in the shadow region. No loss of contrast, no obvious haloing.
(The software is not available to public and perhaps will never be)

The hypothesis we both have is stacking priority. Perhaps Zerene Stacker prioritised the shadow regions, which led to false detail being amplified, casting halos to the overall scene.

Zerene Stacker handles all blue just fine as well:
Image
Link: https://flic.kr/p/2dRkv7Y

I was also able to identify similar problems in an older stack of the same butterfly:
Image
https://flic.kr/p/2bLU1vw

Does anyone else have this problem? Besides cutting the image up into 3 segments and laying it over images with shadow regions, running the stack 3 times, and cutting the results up then stitching them together. Yeah, that's the convoluted (and kind of silly) workout I came up with.

Scarodactyl
Posts: 361
Joined: Sat Apr 14, 2018 10:26 am

Post by Scarodactyl »

This might be a dumb idea for a workaround, but if it only has trouble with green could you invert the colors pre stack then reinvert post?

rjlittlefield
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Post by rjlittlefield »

Suggestion: remove the checkmark on Brightness, at Options > Preferences > Alignment.

See the recent thread at http://www.photomacrography.net/forum/v ... hp?t=38784 , especially my two posts at http://www.photomacrography.net/forum/v ... 199#243199 and http://www.photomacrography.net/forum/v ... 570#243570 , for more explanation about what I think is happening to you.

There's also a FAQ, as follows:
https://zerenesystems.com/cms/stacker/d ... hy_is_that
My colors changed a little. Why is that?
There are three reasons that output images can have different colors from the input: 1) brightness adjustment, 2) PMax, and 3) “Retain extended dynamic range” when saving. “Brightness adjustment” refers to Zerene Stacker's attempt to correct for uneven exposure between various input images. That feature is turned on by default, but you can turn it off by un-checking Brightness at Options > Preferences > Alignment. “PMax” refers to the PMax stacking method, which often makes slight changes in brightness, contrast, and saturation as a side effect of doing its focus stacking. This behavior is an unavoidable side effect of PMax and should be considered as one of the tradeoffs of PMax versus DMap. “Retain extended dynamic range” when saving causes the range of internal pixel values to be compressed if necessary to fit within the 0-255 range of image files. Internally the range can exceed 0-255 as a result of PMax, brightness adjustment, or even just pixel interpolation during alignment.

Color/brightness/contrast changes can be completely avoided by using the DMap stacking method, with Brightness adjustment turned off at Options > Preferences > Alignment, and “Retain extended dynamic range” turned off at Options > Preferences > Image Saving or in the file save dialog.
--Rik

Macro_Cosmos
Posts: 681
Joined: Mon Jan 15, 2018 9:23 pm
Location: Sydney

Post by Macro_Cosmos »

rjlittlefield wrote:Suggestion: remove the checkmark on Brightness, at Options > Preferences > Alignment.

See the recent thread at http://www.photomacrography.net/forum/v ... hp?t=38784 , especially my two posts at http://www.photomacrography.net/forum/v ... 199#243199 and http://www.photomacrography.net/forum/v ... 570#243570 , for more explanation about what I think is happening to you.

There's also a FAQ, as follows:
https://zerenesystems.com/cms/stacker/d ... hy_is_that
My colors changed a little. Why is that?
There are three reasons that output images can have different colors from the input: 1) brightness adjustment, 2) PMax, and 3) “Retain extended dynamic range” when saving. “Brightness adjustment” refers to Zerene Stacker's attempt to correct for uneven exposure between various input images. That feature is turned on by default, but you can turn it off by un-checking Brightness at Options > Preferences > Alignment. “PMax” refers to the PMax stacking method, which often makes slight changes in brightness, contrast, and saturation as a side effect of doing its focus stacking. This behavior is an unavoidable side effect of PMax and should be considered as one of the tradeoffs of PMax versus DMap. “Retain extended dynamic range” when saving causes the range of internal pixel values to be compressed if necessary to fit within the 0-255 range of image files. Internally the range can exceed 0-255 as a result of PMax, brightness adjustment, or even just pixel interpolation during alignment.

Color/brightness/contrast changes can be completely avoided by using the DMap stacking method, with Brightness adjustment turned off at Options > Preferences > Alignment, and “Retain extended dynamic range” turned off at Options > Preferences > Image Saving or in the file save dialog.
--Rik
Thanks! That fixed the issues. I'll probably have it unchecked from now. I use constant lighting, would like to know exactly why it happened. I'll rerun the stack and follow the outline provided in your response on the other thread to see what's going on.

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