[yt-users] Strange Behaviour in ProjectionPlot
Patrick Rieser
patrick.rieser at uibk.ac.at
Tue Nov 13 06:19:13 PST 2012
Thanks for fixing it so fast, you people are really incredible!
Best wishes,
Patrick
Am 13.11.2012 15:15, schrieb Matthew Turk:
> Hi Patrick,
>
> I've pushed a fix in 3b328da941be:
>
> https://bitbucket.org/yt_analysis/yt/changeset/3b328da941be8637737b0405e57d6222
>
> If you run "yt update" you should get it. Thanks for catching this!
>
> -Matt
>
> On Tue, Nov 13, 2012 at 9:11 AM, Patrick Rieser
> <patrick.rieser at uibk.ac.at> wrote:
>> Yes, it's a flash dataset.
>>
>>
>> Thanks a lot!
>>
>> Best wishes,
>> Patrick
>>
>> Am 13.11.2012 15:07, schrieb Matthew Turk:
>>
>> Hi Patrick,
>>
>> Is this a FLASH dataset, by any chance? If so, I think I know the problem
>> for why it is not adding the units. I will take a look and get back to you.
>>
>> Matt
>>
>> On Nov 13, 2012 9:00 AM, "Patrick Rieser" <patrick.rieser at uibk.ac.at> wrote:
>>> mpccm doesn't seem to be in the output. Do I have to set a switch
>>> somewhere so that it is created?
>>>
>>>
>>> level # grids # cells # cells^3
>>> ----------------------------------------------
>>> 0 1 4096 15
>>> 1 8 32768 31
>>> 2 64 262144 63
>>> 3 512 2097152 127
>>> 4 512 2097152 127
>>> 5 512 2097152 127
>>> 6 512 2097152 127
>>> 7 512 2097152 127
>>> ----------------------------------------------
>>> 2633 10784768
>>>
>>>
>>> t = 3.03585620e+17 = 3.03585620e+17 s = 9.62004779e+09 years
>>>
>>> Smallest Cell:
>>> Width: 4.883e-04 unitary
>>> Width: 1.562e-02 mpc
>>> Width: 1.562e+01 kpc
>>> Width: 1.562e+04 pc
>>> Width: 3.223e+09 au
>>> Width: 6.934e+11 rsun
>>> Width: 2.995e+17 miles
>>> Width: 4.821e+22 cm
>>> Width: 4.821e+22 1
>>>
>>>
>>> Best wishes,
>>> Patrick
>>>
>>> Am 13.11.2012 14:55, schrieb Matthew Turk:
>>>> Hi Patrick,
>>>>
>>>> It gets autocreated by concatenating "mpc" with "cm", so it won't show
>>>> up directly in the source. If you run pf.h.print_stats() it will
>>>> print out all the available length units -- what shows up in there?
>>>>
>>>> -Matt
>>>>
>>>> On Tue, Nov 13, 2012 at 7:55 AM, Patrick Rieser
>>>> <patrick.rieser at uibk.ac.at> wrote:
>>>>> When I try
>>>>>
>>>>> pc.set_width((28,'mpccm'))
>>>>>
>>>>> it raises a key error:
>>>>>
>>>>>
>>>>> Traceback (most recent call last):
>>>>> File "projections.py", line 89, in <module>
>>>>> pc.set_width((28,'mpccm'))
>>>>> File
>>>>>
>>>>> "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
>>>>> line 81, in newfunc
>>>>> rv = f(*args, **kwargs)
>>>>> File
>>>>>
>>>>> "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
>>>>> line 458, in set_width
>>>>> width = [w / self.pf[unit] for w in width]
>>>>> File
>>>>>
>>>>> "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",
>>>>> line 143, in __getitem__
>>>>> raise KeyError(key)
>>>>> KeyError: 'mpccm'
>>>>>
>>>>>
>>>>> Also when I search through the yt source code, "mpccm" is only found in
>>>>> universal_fields.py (in the WeakLensingConvergence field) and in
>>>>> light_ray.py.
>>>>>
>>>>> Best wishes,
>>>>> Patrick
>>>>>
>>>>>
>>>>> Am 12.11.2012 20:32, schrieb Britton Smith:
>>>>>
>>>>> Patrick,
>>>>>
>>>>> Don't worry about it. I do that stuff all the time.
>>>>>
>>>>> Britton
>>>>>
>>>>>
>>>>> On Mon, Nov 12, 2012 at 2:26 PM, Patrick Rieser
>>>>> <patrick.rieser at uibk.ac.at>
>>>>> wrote:
>>>>>> Ah damn, now I feel stupid. I should have realized that. I will try it
>>>>>> tomorrow, but yes, that should fix it!
>>>>>>
>>>>>> Thanks a lot!
>>>>>>
>>>>>> Best wishes,
>>>>>> Patrick
>>>>>>
>>>>>> Am 12.11.2012 19:38, schrieb Nathan Goldbaum:
>>>>>>
>>>>>>> If Britton is correct (and looking closely at your script, I suspect
>>>>>>> he
>>>>>>> is) you'll likely fix the issue by specifying the width of the image
>>>>>>> in
>>>>>>> comoving units:
>>>>>>>
>>>>>>> pc.set_width((28,'mpccm'))
>>>>>>>
>>>>>>> Right now the plot axes will still choose to annotate the x and y axes
>>>>>>> using physical units, even though the width of the image will be the
>>>>>>> comoving width you requested. Sorry for that bit of nonintuitiveness.
>>>>>>> Sam
>>>>>>> Skillman just filed a bug about this issue which I will fix soon:
>>>>>>>
>>>>>>> https://bitbucket.org/yt_analysis/yt/issue/463/plotwindow-axes-unit-defaults
>>>>>>>
>>>>>>> -Nathan
>>>>>>>
>>>>>>> On 11/12/12 10:25 AM, Britton Smith wrote:
>>>>>>>> Hi Patrick,
>>>>>>>>
>>>>>>>> Is this a cosmology simulation? If so, I think the issue is that the
>>>>>>>> window is in physical coordinates, which are increasing with time.
>>>>>>>>
>>>>>>>> Britton
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Nov 12, 2012 at 1:21 PM, Nathan Goldbaum
>>>>>>>> <nathan12343 at gmail.com
>>>>>>>> <mailto:nathan12343 at gmail.com>> wrote:
>>>>>>>>
>>>>>>>> Hi Patrick,
>>>>>>>>
>>>>>>>> I'm unable to reproduce the issue you're seeing. I'm running
>>>>>>>> the
>>>>>>>> following script:
>>>>>>>>
>>>>>>>> from yt.mods import * # set up our namespace
>>>>>>>> from yt.analysis_modules.level_sets.api import *
>>>>>>>>
>>>>>>>> pf = load("galaxy0030/galaxy0030")
>>>>>>>>
>>>>>>>> master_clump = pf.h.load_object('My_Clumps')
>>>>>>>>
>>>>>>>> all_clumps = get_lowest_clumps(master_clump)
>>>>>>>>
>>>>>>>> for i in range(1,3):
>>>>>>>>
>>>>>>>> prj = ProjectionPlot(pf,2,'Density',center='c')
>>>>>>>>
>>>>>>>> prj.set_width((20,'kpc'))
>>>>>>>>
>>>>>>>> slc.annotate_text([0.0,1.05], "Clump %s" % i)
>>>>>>>>
>>>>>>>> slc.annotate_clumps([all_clumps[i]])
>>>>>>>>
>>>>>>>> slc.save(str(i))
>>>>>>>>
>>>>>>>> I've previously saved the clump objects in the file "My_clumps".
>>>>>>>> I did this following Britton's recipe from the workshop:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> https://bitbucket.org/brittonsmith/yt.workshop2012.clump-finding/src/1e7af99cec95fb307bb79055f908d39a200b7091/scripts/find_clumps_and_save.py?at=default
>>>>>>>>
>>>>>>>> When I run the script, I get the following two images:
>>>>>>>>
>>>>>>>> http://i.imgur.com/MhkaQ.png
>>>>>>>> http://i.imgur.com/ZGzTl.png
>>>>>>>>
>>>>>>>> This script uses the IsolatedGalaxy dataset stored at
>>>>>>>> yt-project.org/data <http://yt-project.org/data>
>>>>>>>>
>>>>>>>> It would help me track down what's going wrong if you could come
>>>>>>>> up with a somewhat simpler script that reproduces the error,
>>>>>>>> preferably using one of the datasets on yt-project.org
>>>>>>>> <http://yt-project.org>. Please feel free to e-mail me in
>>>>>>>> private
>>>>>>>> or join us on irc so we can iterate on this.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Nathan
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11/12/12 9:50 AM, Patrick Rieser wrote:
>>>>>>>>
>>>>>>>> Hey all,
>>>>>>>>
>>>>>>>> So I still get some strange behaviour with the
>>>>>>>> ProjectionPlot.
>>>>>>>> If I use the projection.set_width() with the clumps callback
>>>>>>>> method I get the real image shrinked inside the the plot
>>>>>>>> window. Strange thing is, that it grows with each step! Here
>>>>>>>> is a demonstration how it looks (you have to look closely as
>>>>>>>> it doesn't grow that much each step):
>>>>>>>>
>>>>>>>> http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/
>>>>>>>>
>>>>>>>> If I don't use the set_width() then the image itself looks
>>>>>>>> fine, but the scale on the axis grows with each step. So it
>>>>>>>> seems to be the same error than with fixed width.
>>>>>>>>
>>>>>>>>
>>>>>>>> Best wishes,
>>>>>>>> Patrick
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Here is the code that I am using:
>>>>>>>>
>>>>>>>> # ID is just a list of tuples with clumps/their position in
>>>>>>>> an
>>>>>>>> array
>>>>>>>> # sim_files and clump_files is a list containing the
>>>>>>>> filenames
>>>>>>>> # get_myclump() simply returns a specific clump
>>>>>>>>
>>>>>>>> for j, series in enumerate(ID):
>>>>>>>> for i in series:
>>>>>>>> pf = load(sim_files[i[0]])
>>>>>>>> myclump = get_myclump(clump_files[i[0]], i[1])
>>>>>>>>
>>>>>>>> pc = ProjectionPlot(pf, axis, my_field, center =
>>>>>>>> pf.domain_center, weight_field = my_wfield)
>>>>>>>> pc.set_width(28, "mpc")
>>>>>>>> pc.annotate_text([0.0,1.05], "Clump %s" % j)
>>>>>>>>
>>>>>>>> if redshift:
>>>>>>>> pc.annotate_text([0.917,1.05], "z = %0.4f" %
>>>>>>>> pf.current_redshift)
>>>>>>>> if grid:
>>>>>>>> pc.annotate_grids()
>>>>>>>> if fix_scale:
>>>>>>>> pc.set_zlim(my_field,boundaries[0],boundaries[1])
>>>>>>>>
>>>>>>>> pc.set_cmap("Density", "idl01")
>>>>>>>> pc.annotate_clumps(myclump)
>>>>>>>>
>>>>>>>> pc.save('%s/Clump_%s_File_%s_Nr_%s_%s_Projection.png'
>>>>>>>> % (myBASEDIR, j, i[0], i[1], axis))
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