[ImageJ-devel] EuclideanSpace and imagej.display.Display

[Lee Kamentsky]

I'm running into a number of problems with overlays that are caused by 
the fact that the EuclideanSpace is now defined on the Dataset and not 
on the Display used to composite datasets and overlays. There are more 
than a few issues:

    * Trac issue ImageJ 558 - the user takes a Z-stack, multichannel
      image and thresholds it to get a BinaryMaskOverlay and associated
      ROI. The ROI is properly defined in a 4-dimensional space.
      However, when displayed, a single X/Y plane should be sampled and
      displayed, but there is no mechanism to retrieve the plane being
      displayed or the color display mode. The code iterates through the
      entire stack and that's what causes it to update slowly.

    * Datasets have axes which capture the metadata of what a particular
      dimension means. Overlays don't have that.
    * Channels are really categorical, not ordinal - there's no reason
      the red channel is zero, the green is one and the blue is two and,
      with a channel-stack, the DAPI channel in one image might be the
      PI channel in a second. You can properly relate one channel to the
      other through metadata, but overlays don't have that.
    * You might want to composite datasets - take two images and place
      them adjacently. What happens if they have different axes? What
      happens if they have different channel layouts?

So, what I'm thinking is the following:

    * A display represents the EuclideanSpace that's used to composite
      overlays and datasets.  Think of the display as a big
      N-dimensional container and the overlays and datasets float inside
      that container.
          o The display has a set of axes that are the union of all of
            the axes that appear in the view data objects.
          o There are two behaviors for a view object that does not have
            an axis in the space. Perhaps the user selects the behavior?:
                + The value in space outside of a single plane defined
                  by a coordinate location along the axis is nan or null.
                + The value in space along the missing axis is the same
                  at all locations along that axis.
    * A display window holds the information about what plane is being
      displayed and how the channels are composited.
          o The views are asked to display according to the plane
            information. A plane is an interval where the min=max for
            all dimensions but X and Y. The views could construct
            appropriate projectors based on the interval. The display
            window should also control the channel compositing
            information and the views should reference the display
            window's compositing information instead of maintaining
            their own copies.
    * Perhaps there is a SpatialDataObject or perhaps the DataObject is
      always spatial. In any case, the axis information and channel
      metadata should be pushed up the inheritance hierarchy so that
      Overlay has a first-class representation of that and operations
      that generate overlays from datasets copy the information to the
      overlays they create.
    * There is a spectral dimension, but the channel axis doesn't
      capture that. Channels are categorical and should have names so
      they can be matched in the same way that axes are matched.

It's some work to refactor these things, but as the code base grows and 
becomes more entrenched it will become increasingly difficult to 
refactor, so we should do it sooner rather than later. I don't think 
this is much coding at this point and if you look at the code, there are 
places where this organization clarifies some things.

--Lee
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