For most of the mentioned issues there is the control points list, which
allows a fast search for bad control points.

> A way to get a list of image pairs that have points whose distance is more 
> than X sigma 
> beyond the standard deviation would really help as well. Thanks for reading...
There is cpclean, also accessible from the context menu in the image tab, which 
does something very similar.

** Changed in: hugin
       Status: Triaged => Fix Released

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https://bugs.launchpad.net/bugs/997540

Title:
  Usability improvements for many-pictures compositing

Status in Hugin:
  Fix Released

Bug description:
  I have begun the process of using Hugin to stitch together a massive
  (~ 1gigapixel) panorama from some 500 individual photos and have run
  into some painful scaling issues in the process. Most of these can be
  alleviated with relatively minor changes but I'd like to share them:

  * Control points tab
      Change left image, change right image, and refine points / scroll list 
are at practically opposite corners of the screen. Moving the mouse back and 
forth hundreds of times gets old.
      Option to show only images on right tab that already share control points 
with left image please?
      WHY is the list of points a fixed-size widget that forces me to scroll 
practically every time to check for bad control points?

  * Fast preview
      Drag & move, normal - individual mode: The fixed-height (??? >:( !!!!) 
set of image selection buttons means that if it ever acquires a scrollbar, as 
when more than ~80 images are loaded on even the highest resolution display, it 
becomes impossible to click the checkboxes. The new position optimizer seems to 
not go completely retarded when faced with a handful of bad points (better 
preconditioning?) so I no longer really need to do this but it's still a 
thought.
      There needs to be a renormalize/relative/scale option for the colors of 
the connecting lines on the layout tab so that I don't have to click on every 
single one of five hundred red lines to find the ten of them containing 
completely wrong control points.

  A way to get a list of image pairs that have points whose distance is
  more than X sigma beyond the standard deviation would really help as
  well. Thanks for reading...

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