[yt-users] questions on projection

[Semyeong Oh]

Thank you Matt and Geoffrey for the help.
That cleared things up for now.

Best,
Semyeong


On Tue, Aug 20, 2013 at 11:29 AM, Matthew Turk <matthewturk at gmail.com>wrote:

> Hi Semyeong,
>
> On Tue, Aug 20, 2013 at 12:22 AM, Semyeong Oh <semyeongoh at gmail.com>
> wrote:
> > Hi all,
> >
> > I'm new to yt.
>
> Welcome to yt!  :)
>
> > I have questions about making projections of certain region,
> > and inspecting the data returned.
> >
> > I made a cube as follows:
> >
> > import pylab as pl
> >
> > center = [0.5, 0.5, 0.5]
> > halfwidth = 0.005
> > cube = pf.h.region(center, center-pl.ones(3)*halfwidth,
> > center+pl.ones(3)*halfwidth, ['Density'])
> >
> > print min(cube['x']), max(cube['x'])
> > 0.494873046875 0.505126953125
> >
> > When I print cube['x'].shape, I get (10728,).
>
> Yup -- so this is because what you're getting isn't actually a cube,
> but a rectangular prism that (potentially) covers multiple levels of
> resolution.  There are essentially three main types of data objects in
> yt:
>
> 1) Non-spatial data sources (this is unfortunately named, since they
> are "spatial", they are just not 3D-ordered) which return all the data
> points inside a region, in essentially unsorted fashion.  This would
> be things like spheres, regions, disks, etc.  This also includes
> things like slices and projections, as they are essentially unordered
> collections of data.
> 2) 2D objects that are 2D ordered.  The primary type of this object is
> a FixedResolutionBuffer, which can be created from a projection or a
> slice.
> 3) 3D objects that are 3D ordered.  This would be a "covering grid", a
> "smoothed covering grid" or a "grid" object.
>
> (More along these lines can be found here:
>
> http://yt-project.org/doc/orientation/index.html
>
> including in the "How yt thinks about data" section, but there is some
> discussion in the bootcamp materials as well.)
>
> There are a few reasons for this, the main one of which is that *many*
> but not *all* operations don't require spatial ordering.  As an
> example, often we want to find out the mean value in a region, or the
> center of mass, or something like that, we don't typically need to
> know the 3D ordering (as long as we can also have the 3D positions,
> which we can through the 'x' 'y' 'z' fields).
>
> So to get an actual 3D ordering -- which sometimes we need when doing
> FFTs or whatever -- you can use a covering grid.  I'll talk below a
> bit about getting 2D orderings.
>
> > I tried to make a projection of this cube along z-axis as follows:
> >
> > proj2 = pf.h.proj(2, 'Density', center=center, source=cube)
> >
> > But I could not understand what is returned.
> >
> > print min(proj2['p
> > x']), max(proj2['py']), proj2['px'].shape
> > 0.00390625 0.99609375 (19648,)
> >
> > print proj2['Density']
> > [ 0.  0.  0. ...,  0.  0.  0.]
> >
> > My questions are:
> > 1. What exactly is returned in proj2? Why does it span from 0. to 1.
> when I
> > specified source=cube?
>
> a) proj2 is the "projection" but it's a data source like any other.
> The special fields, "px", "py" are the "pixel" centers, in the x/y
> plane of the projection.  Typically, to convert this below
>
> b) It runs from 0 .. 1 (but with zero as the value outside the cube)
> because the projection algorithm utilizes a quadtree that is
> initialized to the dimensions of the domain in the image plane.  So if
> you have pf.domain_dimensions = [256, 256, 256] the quadtree will
> initialize with [256, 256] root nodes.  But, none of those outside the
> cube will have non-zero values.
>
> >
> > 2. I also tried 'data_source=cube' instead of 'source=cube'. It did not
> > raise any error, and returned
> > something different: array of same shape, but with different data values.
> > Is this keyword also used
> > for projection object? Is there a consistent difference between the two
> > keywords in yt?
>
> This is a weak point in yt we have corrected in the
> (backwards-incompatible) yt-3.0.  I am upset that this distinction has
> persisted, as "data_source", which is used almost everywhere, is then
> passed through as a "field_parameter" rathert than anything else.
> This is something I am embarrassed about and we have changed it for
> the future, but right now it's an ugly point.
>
> (Perhaps for our final 2.x release we should fix this.)
>
> >
> > 3. I could not find documentation on some fields like 'px', 'py' that
> seem
> > to be generated for certain data containers
> > (e.g., 't' for ray objects). Is there an exhaustive list of such fields
> in
> > the documentation?
>
> There is an exhaustive list for derived fields, but these are what
> would be considered "field container" fields and are only documented
> as needed in the docs, i.e., as related to other concepts.  These are
> px, py, pdx, pdy, which are the pixel centers and half-widths (not
> full-widths) in the image plane.  For rays, t is the integration
> parameter, such that "t * vec + start_position = final_position"
> normalized such that t = 1.0 gives final_position.
>
> As I mentioned above, to convert projections and slices (and cutting
> planes) into 2D arrays, you can use either the .to_frb() function (see
> help(proj2.to_frb) for more info) or the .to_pw() function.  These two
> functions take the variable-resolution data sources and turns them
> into 2D arrays.  The second one, to_pw, turns into a plot window
> suitable for easy plotting.  The first one, to_frb, turns it into a
> FixedResolutionBuffer which can be queried to return any field in the
> bounds specified.
>
> Hope that helps, and please write back with any further questions!
>
> -Matt
>
> >
> > Thanks in advance.
> >
> > Semyeong
> >
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