[yt-users] Error in visualization with new derived field

[Jun-Hwan Choi]

Thank you very much Nathan and Sam.
The python always provides simple way to calculate.

Junhwan
On 10/04/12 17:11, Sam Skillman wrote:
> I think you want to first copy the data, or else you may end up 
> modifying the original Density data.
>
> def _DensityCeiling(field, data):
>     Ceiling = 1e-22
>     new_dens = data["Density"].copy()
>     new_dens[new_dens > Ceiling] = Ceiling
>     return new_dens
>
> Cheers,
> Sam
>
> On Thu, Oct 4, 2012 at 3:06 PM, Nathan Goldbaum <nathan12343 at gmail.com 
> <mailto:nathan12343 at gmail.com>> wrote:
>
>     Hi Junhwan
>
>     In fact, in general you'll get back a 1D array.  These are the
>     collapsed values for the data in a single grid (i.e. flattened
>     from 3D to 1D).
>
>     Since your field does not explicitly depend on the 3D nature of
>     the grid, this is an easy fix:
>
>     def _DensityCeiling(field, data):
>         Ceiling = 1e-22
>         wh = np.where(data["Density"] < Ceiling)
>         DensityCeiling = data["Density"]
>         DensityCeiling[wh] = Ceiling
>         return DensityCeiling
>
>     Here np is how I've imported numpy locally.  There may be an even
>     cleverer way of doing the array manipulation that someone else on
>     the list may know of off-hand.
>
>     Cheers,
>
>     Nathan
>
>     On Oct 4, 2012, at 2:00 PM, Jun-Hwan Choi wrote:
>
>>     Hi yt-users,
>>
>>     I try to make a density projection of my simulation.
>>     I would like to make a small modification that if the cell
>>     density higher than a given density ceiling the density value
>>     becomes the density ceiling.
>>     And, I made a following script:
>>     ############################################
>>     from yt.mods import *
>>     import matplotlib.pylab as pylab
>>
>>     def _DensityCeiling(field, data):
>>         Ceiling = 1e-22
>>         nx, ny, nz = data["Density"].shape
>>         DensityCeiling =  na.zeros(data["Density"].shape,
>>     dtype='float64')
>>         DensityCeiling = data["Density"]
>>         for ix, in range(0,nx):
>>             for iy, in range(0,ny):
>>                 for iz, in range(0,nz):
>>                     if(data["DensityCeiling"][ix,iy,iz] > Ceiling):
>>                         DensityCeiling[ix,iy,iz] = Ceiling
>>         return DensityCeiling
>>     add_field("DensityCeiling", function=_DensityCeiling,
>>     units=r"\rm{g}/\rm{cm^3}")
>>
>>
>>     # load up a dataset
>>     pf = load("DD0000/DD0000")
>>     all_center = [0.5, 0.5, 0.5]
>>
>>     pc = PlotCollection(pf,center=all_center)
>>     pc.add_slice("DensityCeiling", 0)
>>     pc.add_slice("DensityCeiling", 2)
>>     pc.add_projection("DensityCeiling", 0)
>>     pc.add_projection("DensityCeiling", 2)
>>
>>     pc.set_width(6, 'kpc')
>>     pc.save("cen_t%04.1f_L6K" % pf.current_time)
>>     pc.set_width(1, 'kpc')
>>     pc.save("cen_t%04.1f_L1K" % pf.current_time)
>>     #######################################################
>>
>>     And then, I got a following error.
>>     File "DenViz.py", line 6, in _DensityCeiling
>>      nx, ny, nz = data["Density"].shape
>>     ValueError: need more than 1 value to unpack
>>
>>     It turns out that the data["Density"] is not always 3d array but
>>     sometimes become 1d array.
>>     Is there any way to fix the derived field to avoid this problem?
>>
>>     Thank you in advance,
>>     Junhwan
>>
>>
>>     -- 
>>     --------------------------------------------------------------
>>     Jun-Hwan Choi, Ph.D.
>>     Department of Physics and Astronomy, University of Kentucky
>>     Tel:(859) 897-6737  <tel:%28859%29%20897-6737>         Fax:(859) 323-2846  <tel:%28859%29%20323-2846>
>>     Email:jhchoi at pa.uky.edu  <mailto:jhchoi at pa.uky.edu>    URL:http://www.pa.uky.edu/~jhchoi  <http://www.pa.uky.edu/%7Ejhchoi>
>>     --------------------------------------------------------------
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-- 
--------------------------------------------------------------
Jun-Hwan Choi, Ph.D.
Department of Physics and Astronomy, University of Kentucky
Tel: (859) 897-6737        Fax: (859) 323-2846
Email: jhchoi at pa.uky.edu   URL: http://www.pa.uky.edu/~jhchoi
--------------------------------------------------------------

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