Thanks a lot for you input. I appreciate all this wonderful infrastructure
around Images.jl
Since I am no expert in image coloring I was simply not sure whether
everything is already there or not.
It seems in the case of alpha blending there are some missing parts. I
still do not get how the "Overlay" functions work without an alpha channel
but I will try to understand it.
And yes I mean that kind of interpolation. If have implemented now a
function
colorize{T<:Colorant}(x::Real,wmin::Real,wmax::Real,cmap::Vector{T})
that takes as input a real value and two window parameters that are mapped
to a certain color. And since the Colors.jl package has only RGB colormaps
I have additionally implemented RGBA colormaps. I am currently not sure if
this would fit into the existing package infrastructure...
Cheers,
Tobias
Am Montag, 16. November 2015 12:39:30 UTC+1 schrieb Tim Holy:
>
> On Monday, November 16, 2015 02:25:43 AM Tobias Knopp wrote:
> > After investigating this a little further I found that the key things I
> > am/was missing are:
> > - How to compose two RGBA values a and b. It turns out that this is the
> > "over" operation given by
> >
> > c = alpha*b + (1-alpha)*a
> >
> > if alpha is the alpha channel of b and a has alpha=1. Do I have missed
> it
> > or is the over operation somewhere implemented in a package?
>
> I'm not aware of a package that implements alpha-compositing. Perhaps it
> could
> be added to ColorVectorSpace (which might then need a new name), or
> perhaps
> better it could be its own package. If you're interested in this, I'd
> recommend starting by creating a type that makes it clear whether you're
> working with pre-multiplied alpha or not, see
> https://en.wikipedia.org/wiki/Alpha_compositing#Description
>
> > - The second thing is colormaps that include an alpha channel. This
> allows
> > to overlay data in a very flexible way. Otherwise its not really clear
> how
> > to compose things
>
> ImageCmap lets you define a colormap that includes an alpha channel, but
> it
> doesn't implement any special operations.
>
> >
> > - The third is: given a colormap, how to interpolate into it (+ window
> > level, window brightness).
>
> Not quite sure what you mean, are you asking if you can have a fractional
> value that lies between two points in the colormap? If the operations you
> want
> to implement can be expressed in terms of + and * via the standard rules
> of
> interpolation, this one should be easy :-): just use Interpolations.jl to
> create the colormap vector, e.g.,
>
> icmap = interpolate(cmap, BSpline(Linear()))
>
> and pass that to ImageCmap. We can easily generalize it to allow an
> AbstractVector.
>
> Note that currently img[i,j] for an ImageCmap returns the index, not the
> color
> value. I don't remember why I did it that way, but I think that's
> something
> that will have to change. Just need to think of the right migration
> strategy.
>
> Best,
> --Tim
>
> >
> > Cheers,
> >
> > Tobias
> >
> > Am Donnerstag, 12. November 2015 21:54:18 UTC+1 schrieb Tim Holy:
> > > On Thursday, November 12, 2015 12:15:46 PM Tobias Knopp wrote:
> > > > Thanks Tim, I tried to look into the code of Overlay but it wasn't
> to
> > >
> > > clear
> > >
> > > > to me. In particular I am missing where the RGB(A) data is combined.
> > >
> > > Here:
> > >
> > >
> https://github.com/timholy/Images.jl/blob/cac28026250814f6ae6594dd26e92707
> > > 6177db60/src/overlays.jl#L60-L67>
> > > > Is it
> > > > really as simple as adding the individual RGB values and preventing
> > > > overflow by clamp?
> > >
> > > Yes.
> > >
> > > > Or is there some infrastructure for color mixing in Colors.jl
> > >
> > > There is, but it's considerably slower. See the ColorVectorSpace.jl
> README
> > > for
> > > discussion.
> > >
> > > > I further looked for functions for gray value mapping
> > >
> > > (Contrast/Brightness)
> > >
> > > > in Colors.jl but could not find anything. This is of course not
> > >
> > > complicated
> > >
> > > > to code but I don't want to miss an existing solution.
> > >
> > > The whole "MapInfo" structure is a very flexible and powerful. Search
> for
> > > it on
> > > this page:
> > > http://timholy.github.io/Images.jl/function_reference.html
> > > From my standpoint, the best feature is that it's "lazy": you specify
> the
> > > transformation you want, but don't execute it until you need it. For
> > > people
> > > like me who routinely browse 1TB images but probably look at <1% of
> the
> > > raw
> > > data in any given dataset (and who also don't have 1TB worth of
> RAM...),
> > > this
> > > is quite an advantage.
> > >
> > > In my own work, I pretty routinely design custom MapInfo types/map
> > > functions
> > > for visualization purposes. For example, I can color individual blobs
> in
> > > each
> > > frame of a movie with something along the lines of
> > >
> > > immutable ColorizeBlobs
> > >
> > > blobpixels::Vector # of length nblobs
> > > blobcolors::Vector{RGB{U8}} # color assigned to each blob
> > >
> > > end
> > >
> > > and passing that to ImageView using the "scalei" keyword argument (a
> > > legacy of
> > > the days when this was called ScaleInfo rather than MapInfo). It's a
> nice
> > > way
> > > of getting custom visualization while leaving all the stupid zoom &
> > > navigation
> > > functionality up to ImageView.
> > >
> > > --Tim
> > >
> > > > Tobi
> > > >
> > > > Am Donnerstag, 12. November 2015 16:42:00 UTC+1 schrieb Tim Holy:
> > > > > Probably the easiest thing would be to just extend the code in
> Images
> > >
> > > and
> > >
> > > > > submit a PR (the code is not very complicated).
> > > > >
> > > > > However, you can do very fancy things with MapInfo objects. This
> is
> > > > > untested,
> > > > > but it should be close:
> > > > >
> > > > > immutable TwoColormap <: MapInfo
> > > > >
> > > > > colormap1
> > > > > colormap2
> > > > >
> > > > > end
> > > > >
> > > > > function map!(dest, mapi::TwoColormap,
> > > > > src::Tuple{AbstractArray,AbstractArray})
> > > > >
> > > > > img1, img2 = src
> > > > > for I in eachindex(dest)
> > > > >
> > > > > dest[I] = clamp(RGBmapi.colormap1[img1[I]] +
> > > > >
> > > > > mapi.colormap2[img2[I]])
> > > > >
> > > > > end
> > > > > dest
> > > > >
> > > > > end
> > > > >
> > > > > --Tim
> > > > >
> > > > > On Thursday, November 12, 2015 07:23:07 AM Tobias Knopp wrote:
> > > > > > Hi,
> > > > > >
> > > > > > I am using the OverlayImage type from the Images.jl package to
> > >
> > > overlay
> > >
> > > > > two
> > > > >
> > > > > > different grayscale images (tomographic data).
> > > > > > If I understand it correctly OverlayImage is restricted to
> colormaps
> > > > >
> > > > > that
> > > > >
> > > > > > go from black to a certain RGB value. Has anybody an idea how
> this
> > >
> > > could
> > >
> > > > > be
> > > > >
> > > > > > extended to Colormaps provided by Colors.jl?
> > > > > >
> > > > > > So my need is:
> > > > > > Input: two 3D datasets (FloatingPoint) + two Colormaps +
> WindowWidth
> > > > > > WindowLevel for each
> > > > > > Output: Combined 3D dataset as RGBA values.
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > Tobias
>
>
