[yt-users] Problem with zlim setting in yt slices

Eric Hallman Eric.Hallman at colorado.edu
Tue Sep 15 12:46:53 PDT 2009


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)
> _______________________________________________
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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/

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