[yt-users] cannot SlicePlot() using cut_region() filter on data from yt.load_uniform_grid()

[Nathan Goldbaum]

Hi Dale,

You should be able to make a SlicePlot with a cut_region data object. I’m
not sure what’s going wrong exactly based on the information in your
e-mail. It’s possible you’ve hit a yt bug.

Check whether you’re using the newest release of yt, version 3.4.0.

If you can send us a self-contained script that reproduces the issue you
are having that will make it easier to see what exactly is going wrong.

In your script either load fake data generated in the script or use a data
file which you can share with the “yt upload” bash command helper. This
will print out a url once the upload is finished that you can include in
your reply so others can download the file and reproduce your issue.

Nathan



On Sun, Dec 10, 2017 at 3:05 PM Dale Braden <genghis17 at comcast.net> wrote:

> Hello,
>
> I have some density data in an unsupported format which I read into yt
> by means of the yt.load_uniform_grid() function.  I want to filter this
> data by creating a cut_region and then do a SlicePlot on the filtered
> data.  What I find is that no matter how I define the cut_region, the
> dynamic range of the resulting plot is said to be 0.0, even though the
> cut region has no values in it which are actually 0.0.
>
> I do not have this problem if I use data in a supported format. For
> example, I can follow the yt tutorial which creates a SlicePlot from a
> cut_region on the Enzo_64 example dataset.  So I wonder if maybe the
> problem I'm having is due to the fact that when one creates a dataset
> using load_uniform_grid(), one ends up with a StreamDataset object
> instead of an object representing a supported format.
>
> Here is some relevant output from my session (omitting the code to read
> in my data from disk):
>
> In [8]: data2 = np.array(griddata)
> In [9]: arr = data2.reshape((41,56,47))
> In [10]: data = dict(density = (arr,"g/cm**3"))
> In [11]: bbox = np.array([[-4.0,4.2],[-5.5,5.7],[-4.175872,5.22413]])
> In [12]: ds = yt.load_uniform_grid(data, arr.shape, length_unit="cm",
> bbox=bbox)
> yt : [INFO     ] 2017-12-09 15:41:20,781 Parameters:
> current_time              = 0.0
> yt : [INFO     ] 2017-12-09 15:41:20,781 Parameters:
> domain_dimensions         = [41 56 47]
> yt : [INFO     ] 2017-12-09 15:41:20,782 Parameters:
> domain_left_edge          = [-4.       -5.5      -4.175872]
> yt : [INFO     ] 2017-12-09 15:41:20,782 Parameters:
> domain_right_edge         = [ 4.2      5.7      5.22413]
> yt : [INFO     ] 2017-12-09 15:41:20,783 Parameters:
> cosmological_simulation   = 0.0
> In [13]: ds.find_max('density')
> yt : [INFO     ] 2017-12-09 15:48:16,640 Max Value is 5.14618e+01 at
> 0.0999999999999996 -0.0000000000000009 -0.0758711276595738
> Out[13]: (51.4618 g/cm**3, YTArray([  1.00000000e-01, -8.88178420e-16,
> -7.58711277e-02]) code_length)
>
> In [14]: ds.find_min('density')
> yt : [INFO     ] 2017-12-09 15:48:53,392 Min Value is 8.71255e-12 at
> -3.8999999999999999 -5.4000000000000004 -4.0758719787234039
> Out[14]: (8.71255e-12 g/cm**3, YTArray([-3.9       , -5.4       ,
> -4.07587198]) code_length)
>
> So you can see from find_min() that all data values are > 0.0.  I should
> mention that if I do a SlicePlot on ds.all_data(), it looks fine.  But
> if I try a SlicePlot on a cut_region, even one that essentially
> duplicates the entire dataset, then there's nothing to plot even though
> the cut_region does have valid data in it:
>
> In [20]: ad = ds.all_data()
> In [23]: den = ad.cut_region(['obj["density"] > 0.0'])
> In [24]: print den.quantities.extrema([('gas','density')])
> [  8.71255000e-12   5.14618000e+01] g/cm**3
> In [25]: p2 = yt.SlicePlot(ds, 'x','density', center="m", data_source=den)
> yt : [INFO     ] 2017-12-09 15:55:58,155 Max Value is 5.14618e+01 at
> 0.0999999999999996 -0.0000000000000009 -0.0758711276595738
> yt : [INFO     ] 2017-12-09 15:55:58,585 xlim = -5.600000 5.600000
> yt : [INFO     ] 2017-12-09 15:55:58,585 ylim = -4.775872 4.624130
> yt : [INFO     ] 2017-12-09 15:55:58,586 xlim = -5.600000 5.600000
> yt : [INFO     ] 2017-12-09 15:55:58,586 ylim = -4.775872 4.624130
> yt : [INFO     ] 2017-12-09 15:55:58,587 Making a fixed resolution
> buffer of (('gas', 'density')) 800 by 800
> yt : [WARNING  ] 2017-12-09 15:55:58,606 Plot image for field ('gas',
> 'density') has zero dynamic range. Min = Max = 0.000000.
> yt : [WARNING  ] 2017-12-09 15:55:58,606 Switching to linear colorbar
> scaling.
>
> That first warning message is the problem: zero dynamic range. What's
> going wrong?
>
> best wishes,
>
> Dale
>
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