Re: [julia-users] Re: Computing colors of molecules with Julia
This is now implemented in Color.jl; not tagged yet, but you can of course
do Pkg.checkout(Color)
Fun thing to try:
using Interact, Color
@manipulate for m = 1:50, n = 1:100
RGB[RGB(i/m,j/n,0) for i=1:m, j=1:n]
end
On Monday, June 9, 2014 2:07:22 PM UTC-4, Stefan Karpinski wrote:
That does seem like a rather nice solution. Makes sense for matrices too –
displaying a color matrix as a 2D color swatch would be handy.
On Mon, Jun 9, 2014 at 1:54 PM, Steven G. Johnson steve...@gmail.com
javascript: wrote:
Rather than defining a ColorVector type to display color vectors as
rainbow swatches, it might be nice to update the writemime function for
AbstractVector{:ColorValue} in Color.jl
https://github.com/JuliaLang/Color.jl/blob/master/src/display.jl#L19-L50
so
that it displays long vectors more nicely. That is, shrink the width of
the swatch size further for long vectors, e.g. in order to fix the overall
width.
Re: [julia-users] Re: Computing colors of molecules with Julia
wow, that Interact package is interesting... I guess I'll have to start
using IJulia then. I'm still stuck with a Vim session and a Julia terminal.
I tried the checkout version of Color, and it's the same (see attached),
i.e. wrong: the blues should be close to the 400 mark and the reds closer
to the 700. the UV purple and IR black should be closer to the ends than
what we see. Any idea what's going wrong?
Yakir Gagnon
The Queensland Brain Institute (Building #79)
The University of Queensland
Brisbane QLD 4072
Australia
cell +61 (0)424 393 332
work +61 (0)733 654 089
On Tue, Aug 26, 2014 at 4:21 AM, Steven G. Johnson stevenj@gmail.com
wrote:
This is now implemented in Color.jl; not tagged yet, but you can of course
do Pkg.checkout(Color)
Fun thing to try:
using Interact, Color
@manipulate for m = 1:50, n = 1:100
RGB[RGB(i/m,j/n,0) for i=1:m, j=1:n]
end
On Monday, June 9, 2014 2:07:22 PM UTC-4, Stefan Karpinski wrote:
That does seem like a rather nice solution. Makes sense for matrices too
– displaying a color matrix as a 2D color swatch would be handy.
On Mon, Jun 9, 2014 at 1:54 PM, Steven G. Johnson steve...@gmail.com
wrote:
Rather than defining a ColorVector type to display color vectors as
rainbow swatches, it might be nice to update the writemime function for
AbstractVector{:ColorValue} in Color.jl
https://github.com/JuliaLang/Color.jl/blob/master/src/display.jl#L19-L50
so
that it displays long vectors more nicely. That is, shrink the width of
the swatch size further for long vectors, e.g. in order to fix the overall
width.
Re: [julia-users] Re: Computing colors of molecules with Julia
Oh sorry, I vaguely mentioned it in my first reply.
The short answer is:
using Color,Images
n = 500
wl1 = 380.
wl2 = 780.
wl = linspace(wl1,wl2,n)
I = Array(Float64,n,n,3)
for i = 1:n
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
for (j,f) in enumerate([:r,:g,:b])
I[i,:,j] = rgb.(f)
end
end
imwrite(I,a.png)
This results in the attached image. While I'm sure there's a much better
way of getting that done (feel free to show be btw, I'd love to know how to
improve), you can immediately see that the blues and reds are too far close
to each other and that the UV violet and IR black are overly represented.
The long answer is that I used pgfplots with Julia to generate that first
image. So the pgfplots part is this:
\begin{tikzpicture}
\draw (0,0) node {\pgfuseshading{mySpectrum}};
\foreach \x/\xl in {-3/400,-1/500,1/600,3/700}{
\draw[gray] (\x,-.75) -- (\x,-1.25) node[anchor=north,black] {\xl};
}
\node at (0,-2) {Wavelength (nm)};
\end{tikzpicture}
and the julia part is this:
using Color
n = 50
wl1 = 380
wl2 = 780
width = 8
wl = linspace(wl1,wl2,n)
d = linspace(0,width,n)
f = open(spectrum.txt,w)
write(f,\\pgfdeclarehorizontalshading{mySpectrum}{2cm}{\n)
for i = 1:n-1
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
txt = \trgb($(d[i])cm)=($(rgb.r),$(rgb.g),$(rgb.b));\n
write(f,txt)
end
i = n
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
txt = \trgb($(d[i])cm)=($(rgb.r),$(rgb.g),$(rgb.b))}
write(f,txt)
close(f)
xl = [400:100:700]
nxl = length(xl)
wli = wl2-wl1
w = zeros(nxl)
for i = 1:nxl
r = (xl[i]-wl1)/wli
w[i] = width*r
end
w .-= width/2
Yakir Gagnon
The Queensland Brain Institute (Building #79)
The University of Queensland
Brisbane QLD 4072
Australia
cell +61 (0)424 393 332
work +61 (0)733 654 089
On Tue, Aug 26, 2014 at 11:43 AM, Steven G. Johnson stevenj@gmail.com
wrote:
On Monday, August 25, 2014 6:35:43 PM UTC-4, Yakir Gagnon wrote:
I tried the checkout version of Color, and it's the same (see attached),
i.e. wrong: the blues should be close to the 400 mark and the reds closer
to the 700. the UV purple and IR black should be closer to the ends than
what we see. Any idea what's going wrong?
You didn't give any indication of how you made that plot...
Re: [julia-users] Re: Computing colors of molecules with Julia
I looked into xcolor, and the color matching function they implement is
only a rough approximation (page 55 of the xcolor manual), whereas Color.jl
actually matches wavelengths to the CIE standard observer measurements. In
this case, I think Color is more correct. Here's someone else's plot made
from the CIE data that looks close to the Color.jl one:
http://en.wikipedia.org/wiki/Luminosity_function#mediaviewer/File:Srgbspectrum.png
On Monday, August 25, 2014 8:43:13 PM UTC-7, Yakir Gagnon wrote:
Oh sorry, I vaguely mentioned it in my first reply.
The short answer is:
using Color,Images
n = 500
wl1 = 380.
wl2 = 780.
wl = linspace(wl1,wl2,n)
I = Array(Float64,n,n,3)
for i = 1:n
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
for (j,f) in enumerate([:r,:g,:b])
I[i,:,j] = rgb.(f)
end
end
imwrite(I,a.png)
This results in the attached image. While I'm sure there's a much better
way of getting that done (feel free to show be btw, I'd love to know how to
improve), you can immediately see that the blues and reds are too far close
to each other and that the UV violet and IR black are overly represented.
The long answer is that I used pgfplots with Julia to generate that first
image. So the pgfplots part is this:
\begin{tikzpicture}
\draw (0,0) node {\pgfuseshading{mySpectrum}};
\foreach \x/\xl in {-3/400,-1/500,1/600,3/700}{
\draw[gray] (\x,-.75) -- (\x,-1.25) node[anchor=north,black] {\xl};
}
\node at (0,-2) {Wavelength (nm)};
\end{tikzpicture}
and the julia part is this:
using Color
n = 50
wl1 = 380
wl2 = 780
width = 8
wl = linspace(wl1,wl2,n)
d = linspace(0,width,n)
f = open(spectrum.txt,w)
write(f,\\pgfdeclarehorizontalshading{mySpectrum}{2cm}{\n)
for i = 1:n-1
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
txt = \trgb($(d[i])cm)=($(rgb.r),$(rgb.g),$(rgb.b));\n
write(f,txt)
end
i = n
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
txt = \trgb($(d[i])cm)=($(rgb.r),$(rgb.g),$(rgb.b))}
write(f,txt)
close(f)
xl = [400:100:700]
nxl = length(xl)
wli = wl2-wl1
w = zeros(nxl)
for i = 1:nxl
r = (xl[i]-wl1)/wli
w[i] = width*r
end
w .-= width/2
Yakir Gagnon
The Queensland Brain Institute (Building #79)
The University of Queensland
Brisbane QLD 4072
Australia
cell +61 (0)424 393 332
work +61 (0)733 654 089
On Tue, Aug 26, 2014 at 11:43 AM, Steven G. Johnson steve...@gmail.com
javascript: wrote:
On Monday, August 25, 2014 6:35:43 PM UTC-4, Yakir Gagnon wrote:
I tried the checkout version of Color, and it's the same (see attached),
i.e. wrong: the blues should be close to the 400 mark and the reds closer
to the 700. the UV purple and IR black should be closer to the ends than
what we see. Any idea what's going wrong?
You didn't give any indication of how you made that plot...
Re: [julia-users] Re: Computing colors of molecules with Julia
Stand corrected. See attached image for a comparison between the three
scales we've discussed. The one in the background is the Julia one, the one
on the bottom is the one you showed from Wikipedia, and the one on top is
the one from xcolor. You can see that the point where Julia disagrees
most with xcolor is at 440 nm: Julia says 440 nm is violet while xcolor
says it's blue. I grabbed a 440 nm interference filter (I'm in a lab) and
looked. It was violet.
Thanks for your time!
Yakir Gagnon
The Queensland Brain Institute (Building #79)
The University of Queensland
Brisbane QLD 4072
Australia
cell +61 (0)424 393 332
work +61 (0)733 654 089
On Tue, Aug 26, 2014 at 2:29 PM, Daniel Jones danielcjo...@gmail.com
wrote:
I looked into xcolor, and the color matching function they implement is
only a rough approximation (page 55 of the xcolor manual), whereas Color.jl
actually matches wavelengths to the CIE standard observer measurements. In
this case, I think Color is more correct. Here's someone else's plot made
from the CIE data that looks close to the Color.jl one:
http://en.wikipedia.org/wiki/Luminosity_function#mediaviewer/File:Srgbspectrum.png
On Monday, August 25, 2014 8:43:13 PM UTC-7, Yakir Gagnon wrote:
Oh sorry, I vaguely mentioned it in my first reply.
The short answer is:
using Color,Images
n = 500
wl1 = 380.
wl2 = 780.
wl = linspace(wl1,wl2,n)
I = Array(Float64,n,n,3)
for i = 1:n
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
for (j,f) in enumerate([:r,:g,:b])
I[i,:,j] = rgb.(f)
end
end
imwrite(I,a.png)
This results in the attached image. While I'm sure there's a much better
way of getting that done (feel free to show be btw, I'd love to know how to
improve), you can immediately see that the blues and reds are too far close
to each other and that the UV violet and IR black are overly represented.
The long answer is that I used pgfplots with Julia to generate that first
image. So the pgfplots part is this:
\begin{tikzpicture}
\draw (0,0) node {\pgfuseshading{mySpectrum}};
\foreach \x/\xl in {-3/400,-1/500,1/600,3/700}{
\draw[gray] (\x,-.75) -- (\x,-1.25) node[anchor=north,black]
{\xl};
}
\node at (0,-2) {Wavelength (nm)};
\end{tikzpicture}
and the julia part is this:
using Color
n = 50
wl1 = 380
wl2 = 780
width = 8
wl = linspace(wl1,wl2,n)
d = linspace(0,width,n)
f = open(spectrum.txt,w)
write(f,\\pgfdeclarehorizontalshading{mySpectrum}{2cm}{\n)
for i = 1:n-1
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
txt = \trgb($(d[i])cm)=($(rgb.r),$(rgb.g),$(rgb.b));\n
write(f,txt)
end
i = n
xyz = colormatch(wl[i])
rgb = convert(RGB,xyz)
txt = \trgb($(d[i])cm)=($(rgb.r),$(rgb.g),$(rgb.b))}
write(f,txt)
close(f)
xl = [400:100:700]
nxl = length(xl)
wli = wl2-wl1
w = zeros(nxl)
for i = 1:nxl
r = (xl[i]-wl1)/wli
w[i] = width*r
end
w .-= width/2
Yakir Gagnon
The Queensland Brain Institute (Building #79)
The University of Queensland
Brisbane QLD 4072
Australia
cell +61 (0)424 393 332
work +61 (0)733 654 089
On Tue, Aug 26, 2014 at 11:43 AM, Steven G. Johnson steve...@gmail.com
wrote:
On Monday, August 25, 2014 6:35:43 PM UTC-4, Yakir Gagnon wrote:
I tried the checkout version of Color, and it's the same (see
attached), i.e. wrong: the blues should be close to the 400 mark and the
reds closer to the 700. the UV purple and IR black should be closer to
the ends than what we see. Any idea what's going wrong?
You didn't give any indication of how you made that plot...
[julia-users] Re: Computing colors of molecules with Julia
This is really cool. It looks like there are still some issues with syntax highlighting in these notebooks (breaking on triple quoted strings, highlighting unicode characters as errors for example) but this situation should improve greatly once my CodeMirror mode is ready for IJulia. On Monday, 9 June 2014 16:04:45 UTC+1, Jiahao Chen wrote: I've started a blog http://jiahao.github.io/julia-blog/ showcasing a few IJulia notebooks I've been working on over the past few months. Currently the only published post is one of my most recent notebooks on using Color.jl to calculate colors of molecules http://jiahao.github.io/julia-blog/2014/06/09/the-colors-of-chemistry.html from their UV-vis spectra. http://jiahao.github.io/julia-blog/2014/06/09/the-colors-of-chemistry.html IJulia notebooks live in a separate repo: https://github.com/jiahao/ijulia-notebooks This was a fun excursion into my former life as a chemist and hopefully gives people an idea of what you can do with IJulia, Color.jl, Gadfly.jl, SIUnits.jl, and Unicode characters.
