[yt-users] empty plot issue

[Kathy Eastwood]

Hi, Matt

Yes, changing the limits as you suggested, e.g.
C = np.array([0.5,0.5,0.5]) * pf.domain_width + pf.domain_left_edge
LE = np.array([0.0,0.0,0.4]) * pf.domain_width + pf.domain_left_edge
RE = np.array([1.0,1.0,0.6]) * pf.domain_width + pf.domain_left_edge

worked. Thanks!!

kathy


On Wed, Nov 27, 2013 at 7:11 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Kathy,
>
> On Tue, Nov 26, 2013 at 2:41 PM, Kathy Eastwood <kathy.eastwood at nau.edu>
> wrote:
> > Hi, helpful folks. Another issue I have been struggling with, which is
> > similar to this thread
> >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-May/003652.html
> >
> > I am working on some FLASH data with the current version of yt using
> MacOS
> > 10.7.5.  Using this exact same data set, I managed to create some nice
> > phaseplots using spheres centered on the densest spot. However, I now
> want
> > to make some plots for a much larger volume of scientific interest...
> > Here is the code
> >
> > from yt.mods import *
> > %matplotlib inline
> > import matplotlib.pyplot as plt
> > import numpy as np
> > pf = load("Strat_Box_hdf5_plt_cnt_0064")
> > pc = PlotCollection(pf, [0.5, 0.5, 0.5])
> > plane = pf.h.region([0.5,0.5,0.5],[0.0,0.0,0.4],[1.0,1.0,0.6])
> > pc.save("plane_cnt_0064")
>
> Hmm, is there a line missing here, where you create a profile or phase
> object?
>
> >
> > I then get the following error
> >
> > ValueError: Data has no positive values, and therefore can not be
> log-scaled
> >
> >
> > Following the advice in the thread listed above, John Wise suggested
> > "For your "empty" plot, do you have any gas with densities between
> > 1e-26 and 1e-27 g/cm^3 in this sphere?  If there's no gas in this
> >
> > range, then CellVolume will be zero and will give you that error
> > message when it tries to take the log of CellVolume.  If you want
> > to manually inspect the CellVolume field, you can print out the following
> > variable
> > pc.plots[-1].data['CellVolume']
> > which will give you the CellVolume as a function of the x-variable
> > for the last plot you have added to your PlotCollection."
> >
> > The writer did not respond in the next thread, so I'm not sure if
> >
> > this worked.  But when I try it, I get the following:
> > KeyError                                  Traceback (most recent call
> last)
> > <ipython-input-18-71f93f9e2cb6> in <module>()
> > ----> 1 pc.plots[-1].data["CellVolume"]
> >
> > /Users/kde/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in
> > __getitem__(self, key)
> >     160         # This raises a KeyError if it doesn't exist
> >     161         # This is because we explicitly want to add all fields
> > --> 162         return self.field_data[key]
> >     163
> >     164     def __setitem__(self, key, value):
> >
> > KeyError: 'CellVolume'
> >
> > Even though CellVolume is explicitly listed in my list of derived
> fields...
> >
> > Also, I did try the same command for Density rather than CellVolume,
> >
> > and the numbers were in the e-24 g cm-3 range...in fact, all the numbers
> > were exactly the same. So I don't know if I've screwed up my data
> container
> > somehow, or if the density values really are too low?
>
> Well, one thing that immediately comes to mind is that your region
> object looks smaller than what I'm used to in FLASH datasets, which
> are typically in cgs.  If you want to take the relative units
> (relative to the box width) and scale them to be absolute in your
> domain, you could do this like so:
>
> C = np.array([0.5,0.5,0.5]) * pf.domain_width + pf.domain_left_edge
> LE = np.array([0.0,0.0,0.4]) * pf.domain_width + pf.domain_left_edge
> RE = np.array([1.0,1.0,0.6]) * pf.domain_width + pf.domain_left_edge
>
> You can try making a plane again with these C, LE, RE values, but you
> can also check the existing one by looking at
>
> plane["Ones"]
>
> and seeing how many values are returned there.  Do you get anything back?
>
> Hope that helps,
>
> Matt
>
> >
> >
> > any ideas?
> > thanks SO much
> > kathy
> >
> >
> >
> > --
> > Kathy DeGioia Eastwood, Ph.D.
> > Professor of Physics and Astronomy
> > Northern Arizona University
> > Flagstaff, AZ 86011-6010
> > Ph: 928-523-7159   FX: 928-523-1371
> > Kathy.Eastwood at nau.edu
> > deliveries: 602 S. Humphreys St., Bldg 19 Rm 209
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>



-- 
Kathy DeGioia Eastwood, Ph.D.
Professor of Physics and Astronomy
Northern Arizona University
Flagstaff, AZ 86011-6010
Ph: 928-523-7159   FX: 928-523-1371
Kathy.Eastwood at nau.edu
deliveries: 602 S. Humphreys St., Bldg 19 Rm 209
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