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Please help before I self-harm
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johan



Joined: 06 Sep 2011
Posts: 1003

PostPosted: Mon Jul 20, 2015 8:03 am    Post subject: Reply with quote

Hello Koorosh,

I don't have an a6000 myself but I googled it, turns out that 6000*4000 is the large image setting in 3:2 and 6000*3376 is the large image setting in 16:9. So for whatever reason your camera has switched between these. Maybe you had an auto setting somewhere that chose this, or the cam was switched off and came back to a different default?

Fwiw I find it helpful to always explicitly manually set everything rather than leave anything up to the camera to decide, that way you fix what you're getting.

Hope that helps or at least gives some pointer,

-Johan
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Koorosh



Joined: 20 Jun 2014
Posts: 215
Location: London

PostPosted: Mon Jul 20, 2015 12:16 pm    Post subject: Reply with quote

Quote:
Hi Koorosh, the resolution through the mobile app is not the best but can't be adjusted as far as I know. The quality setting affects the images transferred through the app, not the live view itself.


Hi Fergus- that could well be the case. There were two separate settings, one which was to do with image size (2M or original) and another which I presumed was output or something that gave for workability or for image quality. It might have been placebo that I thought the output quality was improved, although it slowed down and did seem somewhat clearer afterwards.

Quote:
GIMP should be able to do this, though from http://www.gimp.org/tutorials/Basic_Batch/ the facility looks more like programming than the graphical interface that Photoshop uses.


Ah GIMP! I shall try that out. Might take a little getting used to but I don't fancy manually rotating each one individually, especially because I'm using the Nikon BE 10x at the moment!

Quote:
The numbers that you've quoted are aspect ratios 3:2 and 16:9, so perhaps in addition to randomly choosing orientation it's also randomly choosing aspect ratio.


I can't work it out either. Perhaps I changed something in the remote app as time went on. I have it set to 16:9 aspect ratio in the camera, and manual operation. Perhaps it's a bug in the remote app? I'm trying another stack shortly so I will let you know if the same problem arises. For my sanity I sincerely hope not. Laughing

Quote:
One good possibility to try is tip your setup slightly so that the view is no longer straight down


How much are we talking? Like a matter of a couple of millimetres or so?

Quote:
But there is a galaxy of other programs to choose from. Here is a list of 86 or 87, for example.


Thank you Chris Smile

Quote:
Does this mean you have tried FastStone Image Viewer?

I was going to recommend that as an excellent free program to try and rotate all the images to the same orientation. You can do it quickly in batches. Whether it's method of rotation will solve your problem I don't know.


I absolutely love the program but couldn't find an option to rotate numerous images, and it would be ideal if I can do so and it works. And yes I used Windows file explorer because I couldn't find a similar way of doing so in FastStone. I'll have another try on there and see how that goes.

Quote:
You can't do the procedure Rik described, but I am curious if he did orient all the images in FastStone and still experienced "orientation" stacking problems.


Sorry I'm a bit lost now, do you mean FastStone can't batch rotate images? Or was Rik's batch command not batch rotation?

Quote:
I don't have an a6000 myself but I googled it, turns out that 6000*4000 is the large image setting in 3:2 and 6000*3376 is the large image setting in 16:9. So for whatever reason your camera has switched between these. Maybe you had an auto setting somewhere that chose this, or the cam was switched off and came back to a different default?


Hi Johan Smile I have got it set on 16:9 aspect ratio and have no idea on earth why it seemed to change mid stack. I suspect it's gypsy-curse-related. I have set up everything manually. Honestly all I can reall think is that perhaps there's some software conflict or possibly that when I disconnected the Kindle as the remote it played the system up. I will try the stack again now and see how I fare.

Probably becomes annoying every post but thank you again all for the continued suggestions and help, I really appreciate it. For what it's worth, I've never been so pleased at the quality of the image produced out of the other side with the 10x BE (I managed to get 30 or so images stacked enough to show the level of detail it captured on the wasp). Unfortunately the 135mm lens I'm using produces slightly more magnification than I'm after currently, but I've yet to find a cheap 10mm lens to hook up.
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Charles Krebs



Joined: 01 Aug 2006
Posts: 5805
Location: Issaquah, WA USA

PostPosted: Mon Jul 20, 2015 1:29 pm    Post subject: Reply with quote

Koorosh,

Rik had suggested:
Quote:
In Photoshop, something like select-all, copy, paste to new image, save as new file, should do the job. If you're not already familiar with batch actions, now would be a good time to learn.


You are not going to copy and paste into a new document in FastStone, but there are operations to rotate multiple images quickly and easily.

The easiest is to simply select the multiple files that need to be re-oriented in the same direction (using "CTRL -click" or "Shift-click") and then click on the appropriate ""Rotate" icon on the top menu bar.

You can also hit F3 (or open TOOLS>"Batch Convert Selected Images"). In the batch conversion dialog box select "Advanced Options". You will find a "Rotate" option tab.
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Koorosh



Joined: 20 Jun 2014
Posts: 215
Location: London

PostPosted: Mon Jul 20, 2015 4:58 pm    Post subject: Reply with quote

Ah I'm with you now. Well there's some good news and some bad news. The good news is that the rotation half works on Zerene. Oddly though, the orientation changes to landscape, but appears to view upside down. I had to mess around for a while flipping it more than once to finally get it rightside up. Any ideas?

The bad news is the camera still haphazardly rotates, although it was only the first ten or so images that were a problem. The output was not massively impressive. I need to master diffusion. I'm using a ping hemisphere over the objective and three lights, but one side was very under exposed. I may need another. I'll post the image when I'm at my laptop tomorrow
tomorrow.

Is there a chance that infinity focus is not infinity focus with the adapter? I have an adapter that claims lenses can but wonder if it isn't definitely right with that lens.
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Chris S.
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Joined: 05 Apr 2009
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Location: Ohio, USA

PostPosted: Mon Jul 20, 2015 6:24 pm    Post subject: Reply with quote

Koorosh wrote:
Oddly though, the orientation changes to landscape, but appears to view upside down. I had to mess around for a while flipping it more than once to finally get it rightside up. Any ideas?

My first bet would be that you are not dealing with a simple situation of landscape vs. portrait orientation, but a set of situations where some images need to be rotated 90 degrees clockwise, and other images, 90 degrees counterclockwise. If this is the case and you apply 90 degree rotation in the same direction for all images, it will be the wrong direction for some of the images, making the resultant image upside down.

This is the sort of situation that caused me to write earlier that I think it is a sound decision for Zerene Stacker not to be the software environment where these issues are resolved. There are lots of good, free tools that handle this sort of task very efficiently, with no need to reinvent the wheel.

Quote:
Is there a chance that infinity focus is not infinity focus with the adapter? I have an adapter that claims lenses can but wonder if it isn't definitely right with that lens.

That chance certainly exists. Fortunately, it is very testable--just put your converging lens on its adapter, on your camera, outside. Look at and photograph some distant object with it. (This is without the objective in place, of course.) You should easily be able to determine if the lens can be focused at infinity, and if so, where the indicators are on focus dial is when at infinity focus on your camera. (Most infinity combinations are tolerant of moderate amounts of deviation from infinity focus of the converging lens, but infinity is definitely the place to start, particularly if you're having problems.)

BTW, a 135mm converging lens is already pretty far from the design point of most 10x infinite objectives, but you've likely already thought about that.

--Chris
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Charles Krebs



Joined: 01 Aug 2006
Posts: 5805
Location: Issaquah, WA USA

PostPosted: Mon Jul 20, 2015 6:41 pm    Post subject: Reply with quote

Koorosh wrote:
Quote:
Ah I'm with you now. Well there's some good news and some bad news. The good news is that the rotation half works on Zerene. Oddly though, the orientation changes to landscape, but appears to view upside down. I had to mess around for a while flipping it more than once to finally get it rightside up. Any ideas?


Probably the best thing to do would be to get a Dropbox account (free up to 2 gig) and put in few stack images that you know are a problem when you try to stack them. You could put them in a folder or ZIP file, and then post the URL to that folder or archive in your Dropbox. Then we can look at them more closely. "Half works", "upside down", "flipping it more than once", "rightside up" may mean something to you looking at the images, but it's nearly impossible for us to troubleshoot it. It would also be helpful to have another group of problem "orientations" that are straight out of the camera, and that you have not "flipped" or rotated at all.
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rjlittlefield
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PostPosted: Mon Jul 20, 2015 9:08 pm    Post subject: Reply with quote

Koorosh wrote:
Oddly though, the orientation changes to landscape, but appears to view upside down. I had to mess around for a while flipping it more than once to finally get it rightside up. Any ideas?

This still sounds like a) your camera is pointing straight down, and b) the camera is deciding orientation based on just the momentary value of its orientation sensor. To get a feel for what's happening, imagine that the camera is pointed straight down at the center of a compass rose, with North pointing upward in the frame. The orientation sensor should be reading "center". But like all sensors it's a bit noisy. So instead of reading "center", it reads "a bit North of center", followed by "a bit South of center", and so on, with random deviations. When the orientation sensor reads slightly North of center, the camera gives you normal landscape. When the orientation sensor reads slightly South of center, it gives you inverted landscape (as if you had mounted the camera on a tripod upside down). Similarly when the orientation sensor reads slightly East/West of center, you get normal or inverted portraits, as if you had shot portraits with the handgrip either up or down.

Quote:
Quote:
One good possibility to try is tip your setup slightly so that the view is no longer straight down

How much are we talking? Like a matter of a couple of millimetres or so?

That depends entirely on how noisy the camera's orientation sensor is. You need to get the device physically tipped enough so that the orientation sensor consistently gets one direction as "this side up". Personally I'd start with something blatant like propping the thing up at 45 degrees to confirm that solves the problem, then start tipping it back down until it messes up again.

Quote:
Charles Krebs wrote:
You can't do the procedure Rik described, but I am curious if he did orient all the images in FastStone and still experienced "orientation" stacking problems.

Sorry I'm a bit lost now, do you mean FastStone can't batch rotate images? Or was Rik's batch command not batch rotation?

Sometimes I hate English. In Charles's sentence, I'm pretty sure that "Rik" and "he" were not intended to refer to the same person. Nothing that I wrote or have done related at all to FastStone, except in the general sense (like all programs) that there are two ways in which FastStone might implement rotation.

--Rik
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Charles Krebs



Joined: 01 Aug 2006
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PostPosted: Mon Jul 20, 2015 9:48 pm    Post subject: Reply with quote

This is all starting to give me a headache! Wink Wink
Quote:

Sometimes I hate English. In Charles's sentence, I'm pretty sure that "Rik" and "he" were not intended to refer to the same person. Nothing that I wrote or have done related at all to FastStone, except in the general sense (like all programs) that there are two ways in which FastStone might implement rotation.


I was "talking" to Chris... so...

Rik = Rik
"he" = Koorosh

Wink
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Chris S.
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PostPosted: Mon Jul 20, 2015 11:43 pm    Post subject: Reply with quote

And a headache for me, too! Very Happy

Let me try to clarify a few things that might be confusing in this thread, even if it means repeating words already written.

Koorosh, it appears that when your camera is pointed straight downward, its orientation sensor produces random outputs, which result in images being recorded with random orientations. Ideally, you would turn off your camera's use of this sensor's output, and the problem would go away. But apparently, your camera does not permit this. Thus, as said, one way you can deal with this problem is orient your camera much closer to horizontal, until the issue disappears. Then, if you wish, move your camera incrementally back toward vertical, noting the point at which the problem recurs. Then return your camera to an orientation just short of this point. This is as Rik described.

Still, a wise macro-stacker tends to keep available, as an optional stage of his workflow, a chance to carefully examine a set of newly-acquired images in a powerful image browsing application, before dragging them into Zerene Stacker as input images. The goal in this step is to make sure that nothing went wrong during image acquisition. Plenty of such things can go wrong, and a solid image browser is the place to see such problems, or choose to shoot the stack again. The image browser built into Windows XP was weak; the image browser built into later versions of Windows has improved, but still lags behind dedicated (even if cost-free) image browsers, such as Irfanview and FastStone Image Browser.

My habit is to use Irfanview, which I suspect would work for your purposes (Koorosh). Irfanview is free and was introduced a long time ago. Accordingly, I long ago adopted into my workflow, got used to its idiosyncrasies, and have continued with it. On the other hand, FastStone Image Browser, also cost-free, either came out later or came to my attention later. Nearly every report I've seen of FastStone Image viewer is positive. Perhaps it has fewer idiosyncrasies. I've but briefly tried it. My sense is that it is very nice software, but offers little for an already-experienced user of Irfanview. But if one is not already accustomed to Irfanview, FastStone Image view might be better. This is a situation where I'd likely counsel an experienced IrfanView user to stay with what he knows, but a new user to learn FastStone image viewer instead. I don't have an authoritative opinion, but I'm not eager to dispute Charlie, who has probably compared these applications much more recently than I have.

The larger point is that you probably want to use FastStone Image Viewer, Irfanview, or some other powerful image browser of your choice to make certain--very, very certain--that your acquired images are all of a match before you use them as inputs to Zerene Stacker. Matched in terms of orientation, image size, aspect ratio, exposure, etc. These are all things that can be well examined and managed within top-quality image-browser software.

Zerene Stacker is at present the best stacking application, so far as I can tell. But solid as it is, I hope it will continue to evolve. If we avoid asking Rik to incorporate features already well-developed in scads of free image browser programs, we may reduce pressure that could divert Rik from software improvements we'll likely find useful, and which only Rik can contribute.

--Chris
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Koorosh



Joined: 20 Jun 2014
Posts: 215
Location: London

PostPosted: Tue Jul 21, 2015 5:21 am    Post subject: Reply with quote

I third the confusion Smile

Ok, I get what was said about the vertical sensor picking up on random orientations. I changed a setting in the camera hoping that, although it was only to rotate images in the camera for display, that it might stop the images from changing to portrait and landscape according to what the sensor read.

And I can understand the confusion with my sentence about roating the images and them taking in Zerene. What meant was, that I was batch converting in Faststone and that the rotations took in Zerene, but the images displayed in the opposite direction to how they were displayed in Faststone. It's a case of, all of the images displaying in landscape the right way up on Faststone were upside down in Zerene, and all of the ones that I altered from portrait to landscape the right way by rotating 90 degrees counter clockwise appeared the right way up in Faststone, and right way. up in Zerene. So my guess is that, as you've stated Rik, that Zerene reads one position and the rest read the other. As mentioned however, a bit of messing around ultimately does save it in the right direction. Eventually....

As for a diagnosis, the link you sent Chris with the worst case scenario of orientation problems, is that the kind of thing to look for in the EXIF data? If so, I will have a look and get myself familiar with some technical stuff Smile

I'm still not at home as I'm working currently, but will post my first stack. I know the 200mm is the ideal tube length, but I've seen your guys ultra beautiful 5x stacks and I would love to get that working Smile if infinity focus is easy to see by that then I think it must be at infinity because I tried it on the camera before and it focused on distant objects. Probably not the best lens as it only goes to f/3.5, but from what you've all told me that isn't a massive issue with the effective aperture when using an objective anyway yes? I think the lighting was the biggest issue, but I'll post it and see what you guys think Smile
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rjlittlefield
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PostPosted: Tue Jul 21, 2015 1:25 pm    Post subject: Reply with quote

Koorosh wrote:
What meant was, that I was batch converting in Faststone and that the rotations took in Zerene, but the images displayed in the opposite direction to how they were displayed in Faststone.

Weird! That seems to imply some incompatibility between the image I/O libraries used by Zerene, and whatever it is that FastStone does. I've made a note to investigate this when I have some time.

Quote:
As for a diagnosis, the link you sent Chris with the worst case scenario of orientation problems, is that the kind of thing to look for in the EXIF data?

Yes. And for looking at what's in there, I strongly recommend exiftool. It's not simple to use, but it's the most powerful thing out there for working with metadata.

By the way, adding some information about "root causes" of the confusion about orientation...

There's a document ECMA TR/98, 1st Edition, June 2009, titled "JPEG File Interchange Format (JFIF)", obtainable through http://www.ecma-international.org/publications/techreports/E-TR-098.htm as http://www.ecma-international.org/publications/files/ECMA-TR/ECMA%20TR-098.pdf. Quoting from the Introduction:
Quote:
This document specifies a file format, referred to as the JPEG File Interchange Format (JFIF), for file-based interchange of images encoded according to the JPEG standard (ITU-T Recommendation T.81 | ISO/IEC 10918-1).

Its treatment of orientation is quite straightforward:
Quote:
8 Image Orientation
In JFIF files, the image orientation is always top-down. This means that the first image samples encoded in a JFIF file are located in the upper left hand corner of the image and encoding proceeds from left to right and top to bottom. Top-down orientation is used for both the full resolution image and the thumbnail image. The process of converting an image file having bottom-up orientation to JFIF must include inverting the order of all image lines before JPEG encoding.

Based on just this specification, it would seem that orientation should be a non-issue.

But then along comes EXIF, which provides metadata that can be embedded inside JPEG (JFIF) files. Lo and behold, EXIF includes an orientation tag. In fact, not being satisified with one orientation tag, it includes a couple of them.

According to exiftool, the JPEG files coming from my Canon T1i camera include tags named IFD0:Orientation and Canon:CameraOrientation. When the camera is set to "Auto rotate Off", IFD0:Orientation is consistently "Horizontal (normal)" regardless of camera orientation, while Canon:CameraOrientation is "Rotate 90 CW" when up points left, "Rotate 270 CW" when up points right, and "Horizontal (normal)", which is reported even when the camera is upside down(?!). When the camera is set to "Auto rotate On", then IFD0:Orientation switches to having the same value as Canon:CameraOrientation.

At present, Zerene Stacker sees all of these images as horizontal, with the image rotating inside the frame in the obvious fashion.

Photoshop, in contrast, sees three of the "Auto rotate On" images as being properly oriented, but the one from the upside-down camera is still displayed upside down. (This is consistent with the EXIF tags -- there seems to be a bug in the camera regarding upside-down.)

It seems that the order of pixels as recorded in the file is identical in all cases, in apparent violation of the JFIF standard as quoted above. No doubt I'm reading the standard incorrectly. Confused

By the way, if you happen to ask exiftool about all the orientation tags that it knows about (-list), you get an even more impressive collection:
Quote:
AnatomicalOrientationType
CameraOrientation
CassetteOrientation
ControlPointOrientation
DiffusionGradientOrientation
DisplaySetPatientOrientation
FaceOrientation
FilmOrientation
ImageOrientation
ImageOrientationPatient
ImageOrientationVolume
LevelOrientation
MiniatureFilterOrientation
OphthalmicImageOrientation
Orientation
Orientation2
OrientationLinkedAFPoint
PanOrientation
PatientOrientation
PatientOrientationCodeSequence
PatientOrientationInFrameSequence
PatientOrientationModifierCodeSeq
PlaneOrientationSequence
RTImageOrientation
SlabOrientation
SpatialOrientation
StoreByOrientation
TransducerOrientation
TransducerOrientationModifierSeq
TransducerOrientationSequence
WedgeOrientation

I assume that a lot of these are specific to medical applications, but I've not tried to track them down.

--Rik
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Chris S.
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PostPosted: Tue Jul 21, 2015 2:51 pm    Post subject: Reply with quote

I wonder if the rotational randomness in Koorosh's files, straight from his camera, is expressed only in the EXIF data, or if the pixel arrays are actually written in different rotations. If the former case is the correct one, perhaps a batch edit on the EXIF data would be easiest and most consistent fix--just pick one set or orientation values, and apply it to all images. (And perhaps the optimal set of orientation values is blank?)

This would seem rather easy to investigate.

Also, Koorosh, I've been assuming you're shooting jpeg, though I don't recall your specifying this. If you're shooting raw and converting, we might want to consider what might be happening during this step, too.

--Chris
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rjlittlefield
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PostPosted: Tue Jul 21, 2015 3:28 pm    Post subject: Reply with quote

I strongly suspect that they're written in different orientations.

If the pixels were all written in the same orientation, then I'd expect the current version of Zerene Stacker to see all the images the same, regardless of what EXIF tags they have attached.

There's a small bit of uncertainty in that expectation because I don't have access to all the source code of the image I/O libraries that ZS uses. But it's a very small bit.

--Rik
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johan



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PostPosted: Wed Jul 22, 2015 2:51 am    Post subject: Reply with quote

Chris S. wrote:
Also, Koorosh, I've been assuming you're shooting jpeg, though I don't recall your specifying this. If you're shooting raw and converting, we might want to consider what might be happening during this step, too.

--Chris


There's something in this, maybe? Turns out that 3:2 is native RAW for a6000 but 16:9 is cropped JPG output. So there is some sort of in-camera truncation to JPG going on, which might be misprocessing if it's being hurried by an electronically controlled short interval process time that forces a shot before the previous processing is done. I do sometimes get something like this. I'd personally be quite tempted to compare three identical short 25 shot stacks in RAW, RAW+JPG and JPG with say 5 and 15s between shots to see if any of these runs made the processing more consistent (for aspect ratio).

Orientation, I can't help, sorry. Except that I've discovered since trying to program an EXIF reader for web JPGs that it is an evolving beast filled with many maker's tags which are manufacturer specific and encrypted, and it might be that some of the data written into there by your new camera has info in the maker's field that isn't being read properly by your older computer software.
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