Haze?

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Deanimator
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Haze?

Post by Deanimator »

In the below image (unused coffee grounds), I notice some haze in the upper portion.

Any clues on the cause?
  • Canon 80D
  • Pentax(?) M42 bellows
  • Amscope 4x finite objective
  • 3 Flashpoint 300 studio strobes
  • Wemacro
  • diffusion disk as shown in the post-fire rig thread in the equipment forum
  • PMax stack of 170 images processed with Zerene
Web_Shrunk_Untitled.jpg
Reflections from the objective?
Stray light in the bellows?

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Scarodactyl
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Re: Haze?

Post by Scarodactyl »

Is this a stack? It looks like a layer missed focus.

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Re: Haze?

Post by Deanimator »

Scarodactyl wrote:
Mon May 03, 2021 1:14 pm
Is this a stack? It looks like a layer missed focus.
PMax stack of 170 images processed with Zerene, 30micron steps.

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Re: Haze?

Post by rjlittlefield »

PMax is relentless about preserving focused detail, so the intermittently-blurred appearance of that bright fiber is very odd.

My best guess is that the bright fiber was moving around somehow, although exactly how, I'm having trouble imagining.

In any case, the solution to this puzzle will be found by using this technique described at https://zerenesystems.com/cms/stacker/docs/faqlist#how_can_i_detect_movement_in_my_stack :
How can I detect movement in my stack?
The easiest way is to “play” the stack as if it were a filmstrip. To do this, just press-and-drag within the list of input files. File selection will track the cursor, while the image shown in the source window will update to match. This makes it easy to quickly find any portion of the stack that you are interested in, and at the same time makes it easy to joggle between two or three frames to identify the exact frame where some problem turns up.

If you have already processed the stack, then you can also put a checkmark on “Show as adjusted” in the input files panel. This will show the source images as they ended up after alignment. This makes it much easier to spot movement of the subject. Of course if you are interested in seeing how stable and well aligned your setup is, you will want to leave “show as adjusted” unchecked so that you're seeing the source images before alignment.

By default, processing the stack also generates a set of highly compressed preview-quality images that can be played more quickly than the original high quality source images. For this reason, it's usually better to put off “playing” your stack until after it's been processed once, unless you have some reason up front to suspect that subject movement may be an issue.
--Rik

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Scarodactyl
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Re: Haze?

Post by Scarodactyl »

Image
See the area I've outlined in white which follows the contours like a topo line--it looks like no in focus shot was taken at that depth.

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Re: Haze?

Post by Deanimator »

rjlittlefield wrote:
Mon May 03, 2021 3:04 pm
PMax is relentless about preserving focused detail, so the intermittently-blurred appearance of that bright fiber is very odd.
Could some of the artifacts be caused by including too many out of focus images?

I reran the stack, excluding the most out of focus images. The right side seems sharper to me:
Web_Shrunk_Rescan PMax.jpg

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Re: Haze?

Post by Deanimator »

I singled out a lone coffee ground, keeping the start and end points much more in focus:
Web_Shrunk_2021-05-03-21.10.30 ZS PMax.jpg

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Re: Haze?

Post by rjlittlefield »

Deanimator wrote:
Mon May 03, 2021 5:39 pm
I reran the stack
Thank you for the second image.

I loaded both images into Photoshop, made them into a layered pair, and did the flash-to-compare trick. Fortunately the two images have the same alignment, so it's very easy to see places where sharpness changes.

It's clear from the flashing comparison that there is least one and possibly several gaps in the focus coverage for the first image. The band that Scarodactyl highlighted is one such place. I see at least a half dozen other places, but I cannot tell whether they occur at the same or different depths.

It's clear from the second image that my earlier guess about movement was not correct.

Instead, what seems to have happened is that, for the first image with the fuzzy bands, some source frames just got omitted from the set that was loaded into Zerene Stacker.

Did you try the "play like a filmstrip" method for investigating the first run? Each gap in focus coverage would have appeared as a sudden jump in what was focused, as you skipped over the gap.

Could some of the artifacts be caused by including too many out of focus images?
No, that would not cause any of the artifacts that have been discussed in this thread.

--Rik

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Re: Haze?

Post by Deanimator »

rjlittlefield wrote:
Mon May 03, 2021 7:01 pm
Did you try the "play like a filmstrip" method for investigating the first run? Each gap in focus coverage would have appeared as a sudden jump in what was focused, as you skipped over the gap.
Yes, that's what made me wonder if I was starting the sequence of exposures too soon and ending it too late.

Please see the single coffee ground image for the radical difference.

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Re: Haze?

Post by rjlittlefield »

I'm struggling to figure out how to provide the best help.

You started this thread by writing
Deanimator wrote:
Mon May 03, 2021 1:11 pm
In the below image (unused coffee grounds), I notice some haze in the upper portion.

Any clues on the cause?
The cause of that problem is now clear: you accidentally omitted some source images while running PMax to make that first picture.

So, moving forward I see two main directions.

First is to figure out exactly how those source frames got omitted, and more generally to figure out how to more quickly spot similar problems if they occur again. For that, I still recommend "play like a filmstrip" as the best available technique. I suggest to practice on stacks that are behaving well, so the differences will stand out more for stacks that do not. Again, with a checkmark on "Show as adjusted", you should see focus moving smoothly all the way from one end of the stack to the other. Any jumps, either laterally or in focus depth, will indicate a problem.

Second is to address your other questions about the effect of extra frames on the front or back. For that, the main guideline is that extra frames seldom have any big effect but it's always safer to remove them. Extra frames will usually increase pixel noise with PMax, and they can cause shifts in overall framing and contrast/brightness. However, extra frames at the front and back will not cause loss-of-detail problems like your first image showed.
Please see the single coffee ground image for the radical difference.
Without guidance, what I see appears to be a much shallower scene, with no obvious problems except some softness at lower right.

When you say "radical difference", what aspects are you referring to?

--Rik

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Re: Haze?

Post by Deanimator »

rjlittlefield wrote:
Tue May 04, 2021 10:37 am
When you say "radical difference", what aspects are you referring to?

--Rik
The absence of the artifacts seen in the previous image. It's a much better stack/image, albeit with far fewer images in the stack.

On the previous image, the only way I can imagine there being missing images would be if the camera shutter just wasn't activated by the Wemacro, something I don't recall ever seeing previously. I didn't watch all 100+ shutter actuations. There were no black images which I used to get on deep stacks when using speed lights.

The other possibility is that Elements is omitting images when I process the RAW files into TIFs, but I've NEVER experienced that before, at least not that I'm aware of.

I'll do another deep stack and see if any issues arise.

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Re: Haze?

Post by rjlittlefield »

Perhaps I have misunderstood, but...

My understanding is that your first and second stacked results (https://www.photomacrography.net/forum/ ... hp?id=3754 and https://www.photomacrography.net/forum/ ... hp?id=3755) used source images from the same acquisition. That is, you shot the stack once but processed it twice.

If that's correct, then exactly what sort of processing did you do each time? If you converted from raw to TIFF only once, then raw conversion is exonerated because the second result does not show focus gaps. In that case the problem was probably caused by omitting some images from the selection when you loaded them into Zerene Stacker for the first run.

What exactly was the workflow that produced the first and second stacked results?

--Rik

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Re: Haze?

Post by Deanimator »

rjlittlefield wrote:
Tue May 04, 2021 3:51 pm
Perhaps I have misunderstood, but...

My understanding is that your first and second stacked results (https://www.photomacrography.net/forum/ ... hp?id=3754 and https://www.photomacrography.net/forum/ ... hp?id=3755) used source images from the same acquisition. That is, you shot the stack once but processed it twice.

If that's correct, then exactly what sort of processing did you do each time? If you converted from raw to TIFF only once, then raw conversion is exonerated because the second result does not show focus gaps. In that case the problem was probably caused by omitting some images from the selection when you loaded them into Zerene Stacker for the first run.

What exactly was the workflow that produced the first and second stacked results?

--Rik
Normal workflow:
  1. Take stack in RAW.
  2. Import RAW files into Elements and make any adjustments (exposure, clarity, etc.).
  3. Batch convert edited RAW files to TIFFs in Elements.
  4. Create new project in Zerene.
  5. Add files.
  6. Process to PMAX and DMAP.
  7. (All files in all steps selected with ctrl-A).
The process for the second image was to merely select fewer of the already existing TIFFs in Zerene, removing the most out of focus images from either end of the stack. The process you suggested was used to try to detect anomalies. I didn't find any.

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Re: Haze?

Post by rjlittlefield »

Hhmm. Yes, that looks pretty foolproof.

So then, a good step in understanding any problem is to reproduce it so that it can be debugged.

Have you tried reproducing the problem shown in the first image?

If you can reproduce that image with the fuzzy bands, using the same images that went into the second image plus some more at the ends, then as the fellow who wrote Zerene Stacker I would really Really like to get a copy of that stack.

Or if it's not reproducible, then of course that would be interesting information also.

--Rik

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Scarodactyl
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Re: Haze?

Post by Scarodactyl »

rjlittlefield wrote:
Tue May 04, 2021 3:51 pm
the second result does not show focus gaps.
I am not sure about this, it is hard to tell with the lower resolution image, but I think I might still be able to see the band I highlighted? I am really not sure though.

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