[julia-users] Re: Computing colors of molecules with Julia

[Mike Innes]

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  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 
>  
> 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.
>

[julia-users] Re: Computing colors of molecules with Julia

[Steven G. Johnson]

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 
 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

[Stefan Karpinski]

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 
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
>  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

[Steven G. Johnson]

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  > 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 
>>  
>> 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

[Yakir Gagnon]

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 
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 
>> 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
>>>  
>>> 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

[Steven G. Johnson]

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

[Yakir Gagnon]

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 
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

[Daniel Jones]

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  > 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

[Yakir Gagnon]

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 
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 
>> 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...
>>>
>>
>>