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