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

[Lee Kamentsky]

On 6/6/2011 10:44 AM, Adam Fraser wrote:
> Hi Lee,
>
> These are great observations, and I agree that the sooner they are 
> addressed the better. I looked at the Skype channel, and it appears 
> there hasn't been much discussion on this, so I figured I'd see if I 
> could get a bit of clarification on a couple things below...
>
>               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.
>
> The former behavior makes sense to me, but I'm having a tough time 
> understanding the latter. Could you give an example?
If someone selects a rectangular region at some Z plane, maybe they mean 
to analyze the region not just at that z-plane but at all z-planes. For 
instance, I have one of those (beautiful) drosophila embryos in 3-d, but 
it's z-planes for the current ImageJ 2.0 release. I draw a rectangle 
around it and want to crop to it. I probably want to get the image at 
its complete depth, not just one plane. The user should be able to choose.
>
>         * 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.
>
> Hrm... it seems to me that Overlays are always spatial, but what about 
> datasets? How are we planning on storing derived data (eg: a table of 
> measurement values)?
I think Dataset is always an image, right?
>
>         * 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.
>
> So the idea that the Display will ask its DataObjects for color 
> information right? I'm thinking about what happens when a dataset has 
> a spectral dimension and a channels dimension... not sure if there's a 
> case for this, or how to handle it.
>
I think that would play out as a spectral dimension with its own axis 
and a categorical channels dimension with its own axis.
> Thanks!
> -Adam

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