cannot SlicePlot() using cut_region() filter on data from yt.load_uniform_grid()
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
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@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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