Agreed. I have tested for log values and it works fine, it's only in linear space... On Sep 15, 2009, at 1:56 PM, Sam Skillman wrote:
Hi Fen and Eric,
Looks like there is definitely something wrong with setting zlim for linear-space plots (especially with negative values). I think it has to do with the way the tick marks are defined in PlotTypes.py, but I'm not quite sure yet. I've done some stuff with set_zlim so I'll take a deeper look but this is definitely a bug.
Best, Sam
On Tue, Sep 15, 2009 at 1:46 PM, Eric Hallman <Eric.Hallman@colorado.edu
wrote: Hear hear. I am working on something right now, which is doing a similar thing. no matter what I set the limits to, it is giving me only a factor of 10 of the data in the color scale. My example is very similar, just using set_zlim...
On Sep 15, 2009, at 1:34 PM, Fen Zhao wrote:
Hi all,
I've recently been having problems setting the colorbar max and min in yt, and would appreciate some help figuring out what the problem might be. Full python code attached at the end, but the important parts are:
pf=lagos.EnzoStaticOutput(thefile) pc = PlotCollection(pf, center=[c1, c2, c3])
plot1=pc.add_slice("B", 0) plot2=pc.add_slice("Density", 0) plot3=pc.add_slice("Velocity_Vorticity1", 0) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) +"large" pc.save(thefile2)
plot1.set_width(haloradius*2,1) plot2.set_width(haloradius*2,1) plot3.set_width(haloradius*2,1) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) + "halo" pc.save(thefile2)
Neither the "large" or "halo" have the colorbar set correctly.
Cheers, Fen
Context of code:
import sys sys.path = ["/usr/work/mturk/local-testing/lib/python2.5/site- packages/"] + \ sys.path
from yt.config import ytcfg; ytcfg["lagos","serialize"] = "False" from yt.mods import *
#import yt.lagos as lagos #import yt.raven as raven #import os.path
def write_out_binned_vals(plot, fn): vals = plot.vals x = plot.x_bins y = plot.y_bins print "Opening",fn, vals.shape, x.shape, y.shape f=open(fn,"w") for i in range(x.shape[0]): for j in range(y.shape[0]): print i,j f.write("%0.5e\t%0.5e\t%0.5e\n" % (x[i],y[j],vals[i,j])) f.close()
#ind=71 #inputDir="/a/wain027/g.ki.ki01/fenzhao/data/nobackup/vorticity/ correct" inputDir="/lustre/ki/orange/fenzhao/vorticity/try2" outputDir="/a/wain027/g.ki.ki01/fenzhao/data/nobackup/vorticity/ analysis/slices/data/images/other" outputName="lustreversion"
start=40 end=40
ind=start
while ind<=end: thefile= inputDir + "/star_%04i.dir/star_%04i" % (ind,ind) output= outputDir + "/" + outputName+ "%04i"
pf=lagos.EnzoStaticOutput(thefile)
timeUnits=pf["years"] DensityUnits=pf["Density"] LengthUnits=pf["cm"] VelocityUnits=pf["x-velocity"]
newred=pf["CosmologyCurrentRedshift"] a=1/(1+newred)
k=1.3806503e-16 c=2.99792e10 e=4.8032068e-10 me=9.1093897e-28 mh=1.66053886e-24
pressure=k*(DensityUnits/mh) density=DensityUnits/mh graddensity=density/LengthUnits gradpressure=pressure/LengthUnits bbunits=(c/e)*graddensity*gradpressure/(density**2)
vorticityUnits=VelocityUnits/LengthUnits alpha=mh*c/e/(1+1e-4)
def Vorticity(field,data): return (((data["Velocity_Vorticity1"]**2)+(data["Velocity_Vorticity2"]**2)+ (data[" Velocity_Vorticity3"]**2))**0.5)*vorticityUnits lagos.add_field("Vorticity", units=r"\rm{s}^{-1}",function=Vorticity)
import numpy as na def B(field, data): return na.clip(alpha*(data["Vorticity"]),1e-30,1e30) lagos.add_field("B", units=r"\rm{Gauss}", function=B)
haloradius=0.013
halo = pf.h.sphere([0.5, 0.5, 0.5], haloradius*2.0) v, i, c1, c2, c3, gi = halo.quantities["MaxLocation"]("Density", lazy_reader=True)
pc = PlotCollection(pf, center=[c1, c2, c3])
plot1=pc.add_slice("B", 0) plot2=pc.add_slice("Density", 0) plot3=pc.add_slice("Velocity_Vorticity1", 0) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) +"large" pc.save(thefile2)
plot1.set_width(haloradius*2,1) plot2.set_width(haloradius*2,1) plot3.set_width(haloradius*2,1) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) + "halo" pc.save(thefile2)
ind=ind+1
#plot=pc.add_slice("B", 0) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu office(s): (303) 735-0129 / (303) 492-7484 http://solo.colorado.edu/~hallman/
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Samuel W. Skillman DOE Computational Science Graduate Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder samuel.skillman[at]colorado.edu _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu office(s): (303) 735-0129 / (303) 492-7484 http://solo.colorado.edu/~hallman/