[yt-users] Slice plot error
Nathan Goldbaum
nathan12343 at gmail.com
Sun Sep 16 15:56:23 PDT 2012
Hi Suoqing,
This error will show up if yt cannot select any data. Recently we
changed the way yt handles 2D FLASH data so it's possible that these
changes have messed up data selection for your setup.
Unfortunately it's difficult to say the exact reason why data
selection is broken without knowing more about your setup.
Can you reply with the output of the 'yt stats' command. Run this
from the command line.
It would also help to see the minimum and maximum z values of your
data. There are a number of ways to do this but a sample script would
look something like this:
pf = load(your_data)
dd = pf.h.all_data()
print dd['z'].min(), dd['z'].max()
Cheers,
Nathan
On Sep 16, 2012, at 2:23 PM, Ji Suoqing <jisuoqing at gmail.com> wrote:
> Hi all,
>
> Yesterday I've updated YT (af06f14fcd9e), but after that I found I got some error in slice plot for 2d FLASH data, in both cartesian and cylindrical cases. In cartesian, the error is:
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> yt : [WARNING ] 2012-09-17 01:19:45,023 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name
> yt : [WARNING ] 2012-09-17 01:19:45,023 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name
> yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: current_time = 1.01787779719e-09
> yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: domain_dimensions = [1280 64 1]
> yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: domain_left_edge = [ 0. 0. 0.]
> yt : [INFO ] 2012-09-17 01:19:45,030 Parameters: domain_right_edge = [ 256. 12.8 12.8]
> yt : [INFO ] 2012-09-17 01:19:45,030 Parameters: cosmological_simulation = 0.0
> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field enuc to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field ar36 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field c12 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field ca40 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field cr48 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field fe52 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field he4 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field mg24 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ne20 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ni56 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field o16 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field s32 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field si28 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ti44 to list of fields
> yt : [INFO ] 2012-09-17 01:19:45,356 Max Value is 4.25001e+07 at 22.7500000000000000 0.8375000000000000 0.5000000000000000 in grid FLASHGrid_0001 ([64 64 1]) at level 0 (45, 33, 0)
> yt : [INFO ] 2012-09-17 01:19:45,401 Making a fixed resolution buffer of (dens) 800 by 800
> Traceback (most recent call last):
> File "slice.py", line 14, in <module>
> p1 = SlicePlot(pf, "z", my_var, origin="left-domain")
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 949, in __init__
> PWViewerMPL.__init__(self, slc, bounds, origin=origin)
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 473, in __init__
> if setup: self._setup_plots()
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 725, in _setup_plots
> self.plots[f].image, cax = self.plots[f].cax)
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py", line 1196, in colorbar
> cb = cbar.Colorbar(cax, mappable, **kw)
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 743, in __init__
> ColorbarBase.__init__(self, ax, **kw)
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 258, in __init__
> self.draw_all()
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 272, in draw_all
> self._process_values()
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 570, in _process_values
> b = self.norm.inverse(self._uniform_y(self.cmap.N+1))
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colors.py", line 948, in inverse
> return vmin * ma.power((vmax/vmin), val)
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py", line 3642, in __mul__
> return multiply(self, other)
> File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py", line 936, in __call__
> if m:
> ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> And in cylindrical case, the error is:
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>>>> from yt.mods import *
>>>> pf=load('relax_hdf5_chk_0000')
> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: current_time = 0.0
> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_dimensions = [256 128 1]
> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_left_edge = [ 0.00000000e+00 -6.55360000e+09 0.00000000e+00]
> yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_right_edge = [ 1.31072000e+10 6.55360000e+09 1.74532925e-02]
> yt : [INFO ] 2012-09-17 01:22:27,083 Parameters: cosmological_simulation = 0.0
>>>> p1 = SlicePlot(pf, 'z', 'dens', origin="left-domain")
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 948, in __init__
> slc = pf.h.slice(axis, center[axis], fields=fields)
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1045, in __init__
> self._refresh_data()
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data
> self.get_data()
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 830, in get_data
> self._generate_coords()
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1079, in _generate_coords
> for grid in self._get_grids():
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 898, in _get_grids
> return ObjectIterator(self, attr='_grids')
> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 102, in __init__
> raise YTNoDataInObjectError(pobj)
> yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it. It may lie on a grid face. Try offsetting slightly.
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> I would very appreciate it if you have any idea on solving these errors.
>
> Best wishes,
> Suoqing
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