[yt-users] Slice plot error
Nathan Goldbaum
nathan12343 at gmail.com
Mon Sep 17 14:17:10 PDT 2012
Hi Suoqing,
Can you update your yt installation and try once again? We've patched a couple of things that might have been causing the issues you were seeing.
Also, I see that you were plotting a variable you defined elsewhere, my_var, in your original test script for the cartesian data. Since I don't know the definition of my_var, I can't say if the fixes we added will prevent the crash you saw.
However, I suspect that the crash was due to the fact that my_var was identical everywhere. I think you will avoid the crash if you set the colorbar limits by hand:
slc.set_zlim('my_var',1e-3,1e3)
for example will tell yt to set the color bar limits to 1e-3, 1e3. If the field is ever less than zero, you might also try defining your field so that yt does not take the log of it when plotting:
add_field('my_var', ..., take_log=False)
Please let us know if these changes have resolve your issue.
Cheers,
Nathan
On Sep 16, 2012, at 4:18 PM, Ji Suoqing wrote:
> Hi Nathan,
>
> Thanks for your prompt response.
>
>> Can you reply with the output of the 'yt stats' command.
>
> (yt-x86_64)[jisuoqing at hpcmanage object]$ yt stats cellular_hdf5_chk_0000
> yt : [INFO ] 2012-09-17 03:22:02,644 Parameters: current_time = 0.0
> yt : [INFO ] 2012-09-17 03:22:02,644 Parameters: domain_dimensions = [1280 64 1]
> yt : [INFO ] 2012-09-17 03:22:02,644 Parameters: domain_left_edge = [ 0. 0. 0.]
> yt : [INFO ] 2012-09-17 03:22:02,645 Parameters: domain_right_edge = [ 256. 12.8 12.8]
> yt : [INFO ] 2012-09-17 03:22:02,645 Parameters: cosmological_simulation = 0.0
> yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field enuc to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field ar36 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field c12 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,655 Adding unknown field ca40 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field cr48 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field fe52 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field he4 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field mg24 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field ne20 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field ni56 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field o16 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field s32 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,656 Adding unknown field si28 to list of fields
> yt : [INFO ] 2012-09-17 03:22:02,657 Adding unknown field ti44 to list of fields
> level # grids # cells
> ------------------------------
> 0 64 262144
> ----------------------------
> 64 262144
>
>
> t = 0.00000000e+00 = 0.00000000e+00 s = 0.00000000e+00 years
>
> Smallest Cell:
> Width: 1.620e-25 mpc
> Width: 1.620e-22 kpc
> Width: 1.620e-19 pc
> Width: 3.342e-14 au
> Width: 7.190e-12 rsun
> Width: 3.106e-06 miles
> Width: 1.953e-03 unitary
> Width: 5.000e-01 1
> Width: 5.000e-01 cm
>
> It seems that the only problem is related with slice plot.
>
> Best wishes,
> Suoqing
>
> On Sep 16, 2012, at 6:56 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>> 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
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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