Questions regarding zerene stacker

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Stephane Savard
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Location: Canada

Questions regarding zerene stacker

Post by Stephane Savard »

I'm currently in the 30 day evaluation period for zerene stacker, and there's a few questions I have not been able to answer through either it's getting started guide (is that the only documentation for it?) or online here in these forums.

1. Is the order of input files important? I am doing hand-held stacks, and the order of the frames (by time shot) are usually not ordered by depth. Should I re-order them inside of ZS in a particular order for better results?

2. When choosing a contrast threshold, what is the meaning of the black areas?

3. What should I be looking for when choosing the contrast threshold? What appears in the getting started guide does not actually appear to make much sense with my stacks. In what looks to be the preview, changing the threshold simply seems to make a difference to the amount of black appearing in the image.

So far, I like the interface, and I've only used it for 4 different stacks (from 2 to 20 frames), but I've had to do major retouching to make the final image look good (either dmap or pmax). I must be something wrong. However most work is tedious at best with the program dumping out to the desktop quite a bit, though I suspect it might be the laptop. Once I get home from vacation, I'll need to evaluate it on my 'real' machine to see how it works there.

rjlittlefield
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Post by rjlittlefield »

Stephane,

Hi! For introduction, I'm the author of Zerene Stacker.
is that the only documentation for it?
http://zerenesystems.com/stacker/docs/HowToUseIt.php is the only documentation for basic controls. There is a video tutorial about retouching, and a separate page regarding synthetic stereo, but there is no in-depth discussion of how the algorithms work.
1. Is the order of input files important? I am doing hand-held stacks, and the order of the frames (by time shot) are usually not ordered by depth. Should I re-order them inside of ZS in a particular order for better results?
When you're using DMap, the frames need to be ordered by depth for best results. Otherwise you're liable to get fuzzy or "swirly" areas as the interpolated depth map passes through OOF frames on its way between sharp areas. If you're using PMax, then order does not matter for the stacking process itself.

With either method, order can affect the quality of alignment and brightness correction because the image that's first in the list essentially becomes the "master" image to which the others get aligned. If the first image is unusually bright, dark, or oddly framed, then the whole stack will get adjusted to match.
2. When choosing a contrast threshold, what is the meaning of the black areas?
Black indicates an area where the image content is too low contrast for the software to tell which frame is in best focus. In those areas, ZS will ignore the image content and determine which frame to use by interpolating from surrounding areas where the contrast is higher.
3. What should I be looking for when choosing the contrast threshold? What appears in the getting started guide does not actually appear to make much sense with my stacks. In what looks to be the preview, changing the threshold simply seems to make a difference to the amount of black appearing in the image.
It is correct that while you're changing the threshold, all you will see changing is the amount of black. Differences to the final image will appear only after you lock in a specific threshold by clicking the OK button, then wait while ZS redoes the interpolation and runs through the whole stack again to re-compose the whole image. This interface is a compromise that provides rough guidance at interactive speed.

Generally the best setting of the slider will show OOF background as black, and in-focus subject as non-black. It's OK to have isolated spots of black in the subject too, since they will be filled in by pixels from the same frames as nearby detail.
I've had to do major retouching to make the final image look good (either dmap or pmax). I must be something wrong.
For handheld stacks, a common problem is that the camera moves a little bit from side to side. This causes various parts of the subject and background to line up a little differently from one frame to another, which results in ghosting. A few people regularly shoot high quality stacks by hand, usually by resting or bracing the camera against something solid. But it's not easy in any case. Most successful stacks come from stable mounts such as a tripod.
the program dumping out to the desktop quite a bit, though I suspect it might be the laptop
This is definitely not normal. I've received no other reports of crashes for months. Please capture whatever information you can, and send it to support@zerenesystems.com . Screenshots are always good.

--Rik

Stephane Savard
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Joined: Thu Jan 14, 2010 7:33 am
Location: Canada

Post by Stephane Savard »

Glad to meet you rjlittlefield,

Then I've seen most of the documentation then; the video on the retouching is what convinced me to try out ZS!

"Swirly" results are a very good description of something I've noticed. I'll try rearranging my stack's order, and try it again.

I wish I could help you with support for the product, but there was nothing to screenshot or errors. The program would simply dissapear and the process died silently. Strangest thing was that restarting the program would show the splash screen, then die immediately. Worse was a blue screen of death after closing the program. However, I've had problems with other software, so I am almost certain it was the laptop.

Thanks for all the help; I'll experiment some more with it with these new ideas and see how it goes.

rjlittlefield
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Post by rjlittlefield »

Stephane Savard wrote:there was nothing to screenshot or errors. The program would simply dissapear and the process died silently. Strangest thing was that restarting the program would show the splash screen, then die immediately. Worse was a blue screen of death after closing the program. However, I've had problems with other software, so I am almost certain it was the laptop.
Scary symptoms, but I agree with your analysis. ZS is a pure Java application. That means it executes within the confines of the Java Runtime Environment, which in turn means it doesn't have enough power and permissions to cause a blue screen if the hardware and system software are working properly. What's unusual about ZS is that it accesses lots of memory -- typically about 1.5 GB. If you're seeing crashes more frequently with ZS than with other apps, one possibility is memory problems. But there's a zillion other things it could be too, with these systems as complicated as they are now. I can offer sympathy, but no solid suggestions. Certainly nothing you could do on travel.

--Rik

Chris S.
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Post by Chris S. »

Stephane,

As someone who fixes a lot of computers (and uses Zerene Stacker), my first thought is that your laptop likely has a problem dissipating heat. This happens with many laptops that are two years old or more, or are operated in an environment with dust or pet hair.

As Rik says, ZS is quite stable. When multiple programs can cause a computer to crash, I generally suspect hardware, and very often, heat is the culprit--especially with laptops. Laptops typically have a narrow pathway through which air is blown by fan to dissipate the heat created when the computer is working. Over time, dust builds up in the heat-dissipating metal fins arrayed within this path, and this dust can greatly retard heat dissipation. When computers get too hot, they tend to crash--often by design, for the protection of the hardware. The harder you work your computer, the more heat it creates--so intensive applications tend to crash more than less intensive ones. This would be consistent even with your crashes that occur when simply opening ZS, if the computer is still hot from prior work.

A good way to test for this sort of thing is to download a free copy of a program called "Prime95" and use it in "torture test" mode. A properly-functioning computer can run a torture test indefinitely without errors. I would consider a system stable only if it could run a torture test for at least 24 hours without error--but from what you are describing, I suspect your laptop might report errors within minutes or even seconds of beginning a torture test.

If a computer is not Prime95 stable--and many are not--then crashes are likely to occur occasionally during light use of the computer, and more frequently in heavy use.

If your laptop passes a Prime 95 torture test, I'd think "software problem" (not ZS itself, but Java, drivers, OS, background software running concurrently, etc.) In the very likely even that it does not pass, I'd think "hardware problem, likely involving heat." In that event, I'd first remove the memory chips and blow any dust off of them with a can of compressed air. I'd blow out the memory slots as well, then reseat the memory and try the test again. While this first step is not very likely to fix the problem, it sometimes does and is quite easy.

More likely, you would need to partly disassemble the laptop and clean the dust out of the cooling system. This is very easy for some models, and pretty hard for others. Some people will suggest using compressed air to blow out any dust without disassembly. Trying that is unlikely to hurt, but in my experience rarely helps. When I disassemble laptops, I often find that dust has formed something like a piece of felt in front of the cooling fins. It is firm and stays together when I remove it--no way could it have been blown out by compressed air.

One additional problem with a few laptops (Dells, in my experience) is that the heat sink isn't in good thermal contact with the CPU. In that case, I pull the heat sink off of the CPU, clean off the old heat sink tape with alcohol or acetone, and put down a bit of high-quality heat sink paste.

None of this is actually as hard as it sounds, unless you have one of the brands of laptop that requires major disassembly to get to the heat sink.

And as Rik said, the problem could be caused by a wide variety of things--but in my experience, at least 90 percent of laptops exhibiting the symptoms you described would be fixed by the steps outlined above.

Good luck!

--Chris

Stephane Savard
Posts: 24
Joined: Thu Jan 14, 2010 7:33 am
Location: Canada

Post by Stephane Savard »

I've been suspecting heat problems for a few days now; especially since the amount of blue screens exploded yesterday when I created a custom power profile that didn't allow my laptop to enter sleep mode. I could barely even boot into Windows XP for a while without crashing out.

The laptop was given to me by my brother-in-law after he got fed up with all it's problems and bad experiences with Toshiba repair shop here in Venezuela. So back in early December I took it apart to try to fix it's main problem with the the power jack - the laptop would be plugged in, but would refuse to recharge the cmos or main battery and so appeared dead. Took it apart short of removing the motherboard or removing the CPU, and could find anything wrong after testing the power jack - power was going through to the motherboard. So I put it back together and since it's been working perfectly good ('cept for the heat buildup).

Didn't notice much dust (laptop hasn't been used much), but I wouldn't rule it out.

Anyway, getting back to Zerene Stacker, did manage to make better use of the app, despite some crashes. I did get better results when my stacks were in correct depth order, and now the 'black' was explained, I've been able to make better decisions on it.

Here's another questions, or rather two...

1. In the options, what is the purpose of the Estimation Radius? i.e. in practice what does this do?

2. Along the same thread... what's the smoothing radius?


A few comments about the program in general. It would be nice to have at least 1-2 steps of undo within the retouching phase. Also, considering that dmap's order of input files is important, allowing drag and drop ordering of the input files would be real nice, especially for hand held shooters.

Still, I find that I need to retouch, but I'm expecting it now, and can see that despite best efforts at shooting the frames, some camera rotation does occur. Still, I'm rather impressed with the program so far (despite crashes). Next week I'll be trying it at home on my desktop and really put it through it's paces.

I'm attaching my latest creation...

Image

There's bit of a focus gap on the back carapace, and the far eye seems somewhat soft to me (strangely since it *should* have been in perfect focus in at least one frame). I also want to see about blurring the left most antenna since I currently find it distracting (leading the eye out of the frame). All things I hope to fix when I get to my usual "production" desktop!

However I'm quite happy with it, my first bug picture showing some nice biology - a beetle protecting it's eggs!

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Post by rjlittlefield »

Stephane Savard wrote: 1. In the options, what is the purpose of the Estimation Radius? i.e. in practice what does this do?

2. Along the same thread... what's the smoothing radius?
Those are perennial problems. Every stacking package has them, they all do pretty much the same thing, and I have yet to see a really understandable explanation of what they do. This one probably won't be either, but here goes...

DMap is a "depth map" algorithm. It has three steps. Step 1 is to identify the single best focused frame at each pixel position, by analyzing pixel values in a small neighborhood around each position. The resulting "depth map image" will have some holes and some errors. Step 2 is to interpolate and smooth the depth map to get rid of the holes and either eliminate or reduce the effect of the errors. Step 3 is to use the final depth map to construct the output image by selecting and averaging pixels from the source images.

Estimation Radius sets the size of the neighborhood for step 1. The best value for Estimation Radius depends on the nature of fine detail in the image. If in-focus parts of the image look fairly crisp at 100%, then values in the range of 3-5 pixels often work well. If the image is noticeably fuzzy at 100% but looks fairly crisp at 50%, then larger values are better, say 6-10 pixels. It's important to note that "fuzzy" refers to the visible detail. If you're photographing a smooth seashell, then the visible detail consists of shell markings that may be quite fuzzy even if you're using a superb lens at low magnification. As a result, a large Estimation Radius may be needed for the shell, even though a hairy leaf shot with exactly the same optics and lighting would be better with a small Estimation Radius.

Smoothing Radius sets the amount of smoothing in step 2. In my experience just setting it to be half the Estimation Radius works fine. In odd cases varying the Smoothing Radius independently can improve the result, but in my opinion most likely your time would be better spent in ways other than messing with Smoothing Radius.
It would be nice to have at least 1-2 steps of undo within the retouching phase.
That's high on the list for future upgrades, probably a couple of months out.
Also, considering that dmap's order of input files is important, allowing drag and drop ordering of the input files would be real nice, especially for hand held shooters.
Added to the list.
Still, I'm rather impressed with the program so far (despite crashes).
Thanks, always nice to hear.
There's bit of a focus gap on the back carapace, and the far eye seems somewhat soft to me (strangely since it *should* have been in perfect focus in at least one frame).
If ZS missed that in a well-focused frame, then support@zerenesystems.com would be very interested to know about it and to get a copy of the stack. To my eye, the fuzzy section of the far eye seems to be about the same depth as the fuzzy section of the carapace, so at the moment I suspect a missing frame.

--Rik

rjlittlefield
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Post by rjlittlefield »

Chris S. wrote:my first thought is that your laptop likely has a problem dissipating heat.
Thanks for posting such a great description of the issue and what to do about it! Half the stuff you mention are things that have never occurred to me.
... The harder you work your computer, the more heat it creates--so intensive applications tend to crash more than less intensive ones.
Good point. ZS definitely qualifies as intensive -- it uses all available cores, and tends to keep them very busy with number-crunching.

--Rik

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