I have been having this problem for years on different platforms on different computers all with the same output issues - just decided I have had enough!
1 - Inaccuracies
Basically when I use the auto align or the automate/ photomerge and select reposition, the output pretty much gets it right all the time, however when I inspect further I see that all the images are slightly off and the only way to solve this is to run auto-align a second or third time, or manually position them correctly after, (or if theres a lot of layers I would split them up but will come onto this as another issue).
For example tiles of a large map will be slightly off by around 50px each and will require further work to fix.
So why can't it get them right first time?
The images I would generally be merging are tiles of the same master image - for example lots of google/bing maps screenshot, cropped to remove any overlays such as scale and navigation bars - or where an online viewer only allows viewing tiles which it renders from a larger image, these can then be repositioned to create a high res version of the entire image - all these images are separate files that are loaded into a stack via photoshop.
This is especially true when using more than 10 or 15 layers to align.
2 - Performance of Auto-Align - Reposition
The second issue I have is performance of auto-aligning of a large amount of layers, my manual method is far more efficient and accurate than the auto-aligns method, this is especially true when aligning many layers (30 and up - sometimes I align up to 200 'tiles')
Photoshop (stupid) method
When there a large number of layers to align and there are in a rough order, (i.e. when img_001 ... img_002 ... img_200 etc are in order, where each image immediately relates to their surrounding layers).
It takes ages and ages (talking days!) for photoshop to do these sort of reposition alignments as it is relating each image to every other image (I assume) and then aligning them.
Manual Method
So I break the layers down into folders with groups of around 15, each one is individually auto-aligned and then merge into its own layer (or a smart object to preserve original tiles).
Then there should be about 15 groups max which then auto-align to each other a lot more efficiently.
Photoshop auto method?
Effectively there should be an option when auto-aligning layers (for repositioning) that says something like "Layers Ordered?" which when checked allows photoshop to only relate each image to its immediately surrounding layers and then building up the image afterwards - similar to my method.
For example theres lots of images but img_055 will only be compared against the range img_050 ... img_060.
Furthermore perhaps photoshop should automatically determine how ordered the images are before comparing each file against every other.
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Remember: these are images that have plenty of overlap and are exact overlaps of each other, yet it still can't do it right!!
It's as if it approximates eveything and the more images you align in one go, the less accurate it gets...
1 - Inaccuracies
Basically when I use the auto align or the automate/ photomerge and select reposition, the output pretty much gets it right all the time, however when I inspect further I see that all the images are slightly off and the only way to solve this is to run auto-align a second or third time, or manually position them correctly after, (or if theres a lot of layers I would split them up but will come onto this as another issue).
For example tiles of a large map will be slightly off by around 50px each and will require further work to fix.
So why can't it get them right first time?
The images I would generally be merging are tiles of the same master image - for example lots of google/bing maps screenshot, cropped to remove any overlays such as scale and navigation bars - or where an online viewer only allows viewing tiles which it renders from a larger image, these can then be repositioned to create a high res version of the entire image - all these images are separate files that are loaded into a stack via photoshop.
This is especially true when using more than 10 or 15 layers to align.
2 - Performance of Auto-Align - Reposition
The second issue I have is performance of auto-aligning of a large amount of layers, my manual method is far more efficient and accurate than the auto-aligns method, this is especially true when aligning many layers (30 and up - sometimes I align up to 200 'tiles')
Photoshop (stupid) method
When there a large number of layers to align and there are in a rough order, (i.e. when img_001 ... img_002 ... img_200 etc are in order, where each image immediately relates to their surrounding layers).
It takes ages and ages (talking days!) for photoshop to do these sort of reposition alignments as it is relating each image to every other image (I assume) and then aligning them.
Manual Method
So I break the layers down into folders with groups of around 15, each one is individually auto-aligned and then merge into its own layer (or a smart object to preserve original tiles).
Then there should be about 15 groups max which then auto-align to each other a lot more efficiently.
Photoshop auto method?
Effectively there should be an option when auto-aligning layers (for repositioning) that says something like "Layers Ordered?" which when checked allows photoshop to only relate each image to its immediately surrounding layers and then building up the image afterwards - similar to my method.
For example theres lots of images but img_055 will only be compared against the range img_050 ... img_060.
Furthermore perhaps photoshop should automatically determine how ordered the images are before comparing each file against every other.
----------
Remember: these are images that have plenty of overlap and are exact overlaps of each other, yet it still can't do it right!!
It's as if it approximates eveything and the more images you align in one go, the less accurate it gets...