Strange behaviour in Zerene Stacker

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pontop
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Location: Uppsala, Sweden

Strange behaviour in Zerene Stacker

Post by pontop »

I am in the process of constructing an automated focus sleigh (will post pictures after some more building this weekend) and made a stack of a sunset moth wing yesterday with my newly acquired Nikon 40X ELWD to test the stability of the rig and its ability to take very small steps (1 µm).
During the stacking process I had some problems with Zerene - which are probably just some setting I got wrong, but I can't figure it out. Here goes:

The stack contains 186 frames. I used Slabberjockey to set up substacks of 12 frames with 3 frames overlap, started the stacking and went to bed. This morning it was far from done, and looking at the progress it looked like it was aligning the whole stack again for each slab - the file highlight went slowly through the whole stack and then the slab was stacked. Surely it shouln only need to align the stack once - or align only the frames included in the slab?

Another problem appeared when I wanted to check if the step size was apropriate or overkill. I set the preferences to stack every 5th frame (no slabbing just a pmax of all), but it seemd to ignore this setting and still went through all frames. And no difference between the results as far as I can tell. Setting the preferences to do every 50th fram confirmed that the setting is indeed ignored.

I must have some setting wrong, but what?

Image

Nikon 40X ELWD 20 cm from sensor on EOS 6D (full frame). Illumination 2X IKEA Jansjö lamps through paper. 4 s exposures. 186 frames at 1µm.

rjlittlefield
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Post by rjlittlefield »

Your problem with the repeated processing sounds like what happens when a batch script ends up referencing the same folder of source images multiple times from tasks in separate batches, as opposed to referencing the folder just once with multiple tasks in a single batch, or from multiple batches using %CurrentProject%.

In the bad case, what happens is that for the first task ZS creates a new project, loads the images, aligns them all, then does the Stack Selected and saves the output file. Then it sees that there's another batch not directed against %CurrentProject%, so it does the whole thing all over again except with different images included in the Stack Selected. This process repeats until all the batches are done.

I'm away from my usual computer right now, and my personal memory isn't good enough with SlabberJockey to tell you what to do. But I'm pretty sure the cure for your problem will lie in exactly what you tell SlabberJockey, rather than any settings in Zerene Stacker. (Background: I'm the fellow who wrote Zerene Stacker, so my personal memory on that side is pretty good though certainly not 100%.)

To diagnose the problem of "Stack every N'th frame" being ignored, I would have to know more about exactly what you did. If you loaded files and did the Align & Stack All (PMax) interactively, then I can't imagine what could have gone wrong. But if there was a batch script involved and you changed the setting interactively, then possibly the script contains parameter settings that overrode what you did interactively.

--Rik

pontop
Posts: 83
Joined: Wed Dec 18, 2013 4:00 am
Location: Uppsala, Sweden

Post by pontop »

I knew I could count on you to help. Thanks.
I did the n'th frame stackings manually after the long slabbing run mentioned. I did not reload the pictures, though. I tried doing that now, and it works just fine now.
Speaking of repeated processes: When doing Dmap stacks the program does a lot of calculations before asking the user to give a setting. I am still not able to get that right in the first go, and also found that different parts of the picture sometimes seem to benefit from different settings. Is there a way to no have to repeat the processing up to the point where this setting is made when I want to try different settings?

rjlittlefield
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Post by rjlittlefield »

pontop wrote:I did the n'th frame stackings manually after the long slabbing run mentioned.
Thanks for the clarification. I'll take a look at that case and see if I can figure out what's going on.
Speaking of repeated processes: When doing Dmap stacks the program does a lot of calculations before asking the user to give a setting. I am still not able to get that right in the first go, and also found that different parts of the picture sometimes seem to benefit from different settings. Is there a way to not have to repeat the processing up to the point where this setting is made when I want to try different settings?
There is not. This feature is often requested, and it's definitely on the to-do list, but it's far enough down in priorities that I have no idea when it will get done.

--Rik

Chris S.
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Post by Chris S. »

Pontop, did Rik's advice clear up your issue with SlabberJockey? As the fellow who wrote SlabberJockey, I think Rik's solution was likely correct--the problem probably lay in what you filled into the "Project folder" entry box (fourth yellow box from the top, shown here). Make sure this points to the folder in which you already saved a Zerene Stacker project file that aligned all your input files. In this case, no more alignment processes need to be--or will be--run.

If you still have a problem, please let me know, either in this thread or by PM. Sorry for my slow reply--it was a busy week.

Cheers!

--Chris

pontop
Posts: 83
Joined: Wed Dec 18, 2013 4:00 am
Location: Uppsala, Sweden

Post by pontop »

Hi Chris

Thanks for the reply. I had the folder containing the tif files in the project folder box, while the project was actually stored in a subfolder inside that folder. Changing that did the trick.

/Bo

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