Thanks Matt, Manually creating the buffer seems to work (though John's approach of setting colormap values seems like it might be cleaner). The commands I ended up using are below. Thanks again! Munier *from yt.mods import ** *import matplotlib.pyplot as plt* *from numpy import log10 as log* * * *fName = "DD0006/test_sim_0006"* *var = "star_density"* *axis = 0* * * *pf = load(fName)* *pf.h* *proj = pf.h.proj(axis,var)* * * *res = [ 1000 , 1000 ]* *c = 0.5* *hw = .02* * * *frb = FixedResolutionBuffer(proj,(c-hw,c+hw,c-hw,c+hw),res,antialias=False) * *plt.imshow( log(frb['star_density'] + 1E-5 ) )* *plt.savefig('tmp')* On Wed, Nov 28, 2012 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Munier,
Ah, my mistake -- to_frb was added in the development branch since our last release, which was in September. You can either update to the development branch (hg up -C yt ; python2.7 setup.py develop ) or used a FixedResolutioBuffer manually (super easy to do).
-Matt
Hi Matt,
The command (on ranger, btw) gives
yt module located at: /share/home/01686/msalem/yt-x86_64/src/yt-hg
The current version of the code is:
--- 6f3c1cf6960d (stable) ---
This installation CAN be automatically updated. Updated successfully.
On Wed, Nov 28, 2012 at 3:30 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Munier,
That's weird, it should be in there. What's the output of "yt instinfo", particularly the hash?
-Matt
On Wed, Nov 28, 2012 at 3:29 PM, Munier Azzam Salem <msalem@astro.columbia.edu> wrote:
Hi Nathan,
Thanks for the tips. I think the fixed-resolution buffer is exactly what I need here. Unfortunately, when I run the command:
frb = proj.to_frb(width, res, center=c)
I get the error
Traceback (most recent call last): File "smllPlt.py", line 16, in <module> frb = proj.to_frb(width,res) AttributeError: 'AMRQuadTreeProj' object has no attribute 'to_frb'
I tried updating my version of yt and deleting any .yt files,
but
the error stuck.
best, Munier
On Wed, Nov 28, 2012 at 2:34 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
Hi Munier,
I suspect that the projection of the particle field is zero in the locations that are colored white in your image. This causes these regions to 'fall off' the bottom end of the logarithmic color bar.
I think you have two options. One would be to use a linear colorbar. You can do this following the instructions here:
http://yt-project.org/doc/faq/index.html#how-do-i-modify-whether-or-not-yt-t...
Another option would be to make the plot by hand using a FixedResolutionBuffer. In this case you would make the projection object by hand, extract the raw image buffer using an FRB, and then make the
On Wed, Nov 28, 2012 at 4:18 PM, Munier Azzam Salem <msalem@astro.columbia.edu> wrote: plot
manually using matplotlib. There's an example in the yt docs that covers how to do this:
http://yt-project.org/doc/visualizing/manual_plotting.html?highlight=manual%...
In the latter case if you want the areas that project to zero to
appear
with a logarithmic colorbar, you'll need to manually set the regions in the FRB that are equal to zero to some small number.
Cheers,
Nathan
On Nov 28, 2012, at 9:29 AM, Munier Azzam Salem wrote:
Hi yt gurus,
I've been making projections of star_density from enzo output files and they seem to be working out fine. However, wherever particles do not exist the background remains white instead of following my chosen colormap. Is there a way to paint these areas to follow the colormap?
thanks! Munier
I've attached an image of what gets plotted, and the relevant bits of my script are:
from yt.mods import *
fName = "DD0006/test_sim_0006" var = "star_density" axis = 0
pf = load(fName) pf.h
pc = PlotCollection(pf) p = pc.add_projection(var,axis) #p.modify["particles"](1.0)
radius = .02;
pc.set_xlim(.5-radius,.5+radius) pc.set_ylim(.5-radius,.5+radius)
pc.save(fName)
-- Munier A. Salem // 845.489.6450
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