On Thu, Oct 4, 2018 at 11:00 AM Kacper Kowalik <xarthisius.kk@gmail.com> wrote:

Hi,
I took a liberty of filing the issue:

https://github.com/yt-project/yt/issues/2048

I ran a git bisect and found the source of the regression.
Cheers,
Kacper

On 10/4/18 7:44 AM, Nathan Goldbaum wrote:
> Hi Stephanie,
>
> No worries, it would still be good to get an issue filed. That’s much
> more actionable for us than a mailing list thread and makes it less
> likely we’ll forget about this.
>
> Nathan
>
> On Thu, Oct 4, 2018 at 7:36 AM Stephanie Tonnesen <stonnes@gmail.com
> <mailto:stonnes@gmail.com>> wrote:
>
> Hi Nathan,
>
> I don’t think I was on the stable version before? But I don’t know
> what my old version was, unfortunately. I might have done Git stash
> on it, so may be able to go back and see....not terribly optimistic
> though....
>
> On Wed, Oct 3, 2018 at 11:41 PM Nathan Goldbaum
> <nathan12343@gmail.com <mailto:nathan12343@gmail.com>> wrote:
>
> Hi Stephanie,
>
> Thanks for reporting the regression. If this works on stable but
> not on dev it’s due to a bug. Can you open an issue on Github?
> We can follow up there.
>
> Nathan
>
> On Wed, Oct 3, 2018 at 10:28 PM Stephanie Tonnesen
> <stonnes@gmail.com <mailto:stonnes@gmail.com>> wrote:
>
> Hi all,
>
> I updated my yt dev so that I could fix a problem with the
> clump finder, and now a simple phaseplot script that I have
> been using is failing. It seems to claim that there is no
> mass in the cut_region I am using, even though there clearly
> is (as shown in total_quantity).
>
> If anyone has some ideas I would really appreciate it!!
>
> Thanks,
> Stephanie
>
> Here is the script:
>
> import sys
> import numpy as np
> import yt
>
> ds =
> yt.load("/mnt/ceph/users/stonnesen/runs/IsolatedGalaxy/galaxy0030/galaxy0030")
> logs = {('index','cylindrical_r'):False}
> logs = {('gas','velocity_z'):False}
> logs = {('gas','velocity_cylindrical_radius'):False}
> logs = {('gas','velocity_cylindrical_theta'):False}
> logs = {('index','z'):False}
>
> ds.index
> ds.field_info['gas','velocity_z'].take_log = False
>
> ad = ds.all_data()
>
> densegas24 = ad.cut_region("obj['density'] > 1e-24")
> densegas5e24 = ad.cut_region("obj['density'] > 5e-24")
> densegas25 = ad.cut_region("obj['density'] > 2e-25")
>
>
> print (ds.field_list)
> print (densegas24.quantities.total_quantity(["cell_mass"]))
>
> plot21 =
> yt.PhasePlot(densegas24,"z","velocity_z",["cell_mass"],weight_field=None)
> plot21.set_unit('z','kpc')
> plot21.save('IG_densegas24_zvz_0030')
>
> __________
> And then the output seems to claim that there is no positive
> values of cell_mass, despite the fact that when I do
> total_quantity I have some mass:
>
> yt : [INFO ] 2018-10-03 23:18:17,529 Parameters:
> current_time = 0.0060000200028298
> yt : [INFO ] 2018-10-03 23:18:17,529 Parameters:
> domain_dimensions = [32 32 32]
> yt : [INFO ] 2018-10-03 23:18:17,530 Parameters:
> domain_left_edge = [ 0. 0. 0.]
> yt : [INFO ] 2018-10-03 23:18:17,530 Parameters:
> domain_right_edge = [ 1. 1. 1.]
> yt : [INFO ] 2018-10-03 23:18:17,531 Parameters:
> cosmological_simulation = 0.0
> Parsing Hierarchy : 100%|ââââââââââ| 173/173 [00:00<00:00,
> 9414.27it/s]
> yt : [INFO ] 2018-10-03 23:18:17,565 Gathering a field
> list (this may take a moment.)
> yt : [WARNING ] 2018-10-03 23:18:20,923 Profiled field
> ('gas', 'cell_mass') has no positive values. Max = 0.000000.
> yt : [WARNING ] 2018-10-03 23:18:20,923 Switching to linear
> colorbar scaling.
> [('all', 'creation_time'), ('all', 'dynamical_time'),
> ('all', 'metallicity_fraction'), ('all', 'particle_index'),
> ('all', 'partic
> le_mass'), ('all', 'particle_position_x'), ('all',
> 'particle_position_y'), ('all', 'particle_position_z'),
> ('all', 'particle_type
> '), ('all', 'particle_velocity_x'), ('all',
> 'particle_velocity_y'), ('all', 'particle_velocity_z'),
> ('enzo', 'Average_creation_ti
> me'), ('enzo', 'Bx'), ('enzo', 'By'), ('enzo', 'Bz'),
> ('enzo', 'Cooling_Time'), ('enzo', 'Dark_Matter_Density'),
> ('enzo', 'Densit
> y'), ('enzo', 'Electron_Density'), ('enzo',
> 'Forming_Stellar_Mass_Density'), ('enzo', 'Galaxy1Colour'),
> ('enzo', 'Galaxy2Colour')
> , ('enzo', 'HII_Density'), ('enzo', 'HI_Density'), ('enzo',
> 'HeIII_Density'), ('enzo', 'HeII_Density'), ('enzo',
> 'HeI_Density'),
> ('enzo', 'MBHColour'), ('enzo', 'Metal_Density'), ('enzo',
> 'PhiField'), ('enzo', 'Phi_pField'), ('enzo',
> 'SFR_Density'), ('enzo',
>   'Star_Particle_Density'), ('enzo', 'Temperature'), ('enzo',
> 'TotalEnergy'), ('enzo', 'gammaHI'), ('enzo', 'kphHI'),
> ('enzo', 'kp
> hHeI'), ('enzo', 'kphHeII'), ('enzo', 'x-velocity'),
> ('enzo', 'y-velocity'), ('enzo', 'z-velocity'), ('io',
> 'creation_time'), ('i
> o', 'dynamical_time'), ('io', 'metallicity_fraction'),
> ('io', 'particle_index'), ('io', 'particle_mass'), ('io',
> 'particle_positi
> on_x'), ('io', 'particle_position_y'), ('io',
> 'particle_position_z'), ('io', 'particle_type'), ('io',
> 'particle_velocity_x'), ('i
> o', 'particle_velocity_y'), ('io', 'particle_velocity_z')]
> 2.02242737915223e+42 g
> Traceback (most recent call last):
>    File "yt_phaseplots_densegas2.py", line 46, in <module>
>    plot21.save('IG_densegas24_zvz_0030')
>    File
> "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/plot_container.py",
> line 93, in newfunc
>    args[0]._setup_plots()
>    File
> "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py",
> line 1077, in _setup_plots
>    fig, axes, cax)
>    File
> "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py",
> line 1559, in __init__
>    zlim, cmap)
>    File
> "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py",
> line 1580, in _init_image
>    self.cb = self.figure.colorbar(self.image, self.cax)
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/figure.py",
> line 1844, in colorbar
>    cb = cbar.colorbar_factory(cax, mappable, **kw)
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/colorbar.py",
> line 1365, in colorbar_factory
>    cb = Colorbar(cax, mappable, **kwargs)
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/colorbar.py",
> line 943, in __init__
>    ColorbarBase.__init__(self, ax, **kw)
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/colorbar.py",
> line 326, in __init__
>    self.draw_all()
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/colorbar.py",
> line 352, in draw_all
>    self._config_axes(X, Y)
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/colorbar.py",
> line 460, in _config_axes
>    self.update_ticks()
> File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/colorbar.py",
> line 377, in update_ticks
>    ticks, ticklabels, offset_string = self._ticker()
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/colorbar.py",
> line 620, in _ticker
>    b = np.array(locator())
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/ticker.py",
> line 2101, in __call__
>    return self.tick_values(vmin, vmax)
>    File
> "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/ticker.py",
> line 2127, in tick_values
>    "Data has no positive values, and therefore can not be "
> ValueError: Data has no positive values, and therefore can
> not be log-scaled.
>
>
> --
> Dr. Stephanie Tonnesen
> Associate Research Scientist
> CCA, Flatiron Institute
> New York, NY
>
> stonnes@gmail.com <mailto:stonnes@gmail.com>
>
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>
> --
> --
> Dr. Stephanie Tonnesen
> Associate Research Scientist
> CCA, Flatiron Institute
> New York, NY
>
> stonnes@gmail.com <mailto:stonnes@gmail.com>
> _______________________________________________
> yt-users mailing list -- yt-users@python.org
> <mailto:yt-users@python.org>
> To unsubscribe send an email to yt-users-leave@python.org
> <mailto:yt-users-leave@python.org>
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