[yt-users] pickle

[Elizabeth Tasker]

Hi Matt and Stephen,

While typing out what Matt asked for, I inadvertently fixed the problem! 
It turns out that the equivalent to:

-------> print(cloudcores[40]["Density"])
yt : [INFO     ] 2011-08-11 13:39:59,985 Getting field Density from 2
[  3.80336226e-23   4.31254788e-23   3.87927154e-23 ...,   1.26533774e-22
   2.13753864e-22   2.74680682e-22]


once pickled and de-pickled into 'core' is:

-------> print(core[40][1]["Density"])
yt : [INFO     ] 2011-08-11 13:38:48,531 Getting field Density from 2
[  3.80336226e-23   4.31254788e-23   3.87927154e-23 ...,   1.26533774e-22
   2.13753864e-22   2.74680682e-22]


since

In [29]: print core[40][0]
-------> print(core[40][0])
GT_BTAccel_256AMR4_PeHeat_sf5_SNe_0301

-------> print(core[40][1])
ExtractedRegion (GT_BTAccel_256AMR4_PeHeat_sf5_SNe_0301): 
_base_region=AMRRegion (GT_BTAccel_256AMR4_PeHeat_sf5_SNe_0301): 
center=[ 16.  16.  16.], left_edge=[ 0.  0.  0.], right_edge=[ 32.  32.  
32.]

As a matter of interest, I couldn't get the yt-approved object storage 
to work. I just got:

In [14]: pf.h.save_object("cloudcores", "myclouds")
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>()
----> 1
      2
      3
      4
      5

AttributeError: 'NoneType' object has no attribute 'h'

I tried also:

In [15]: dd.save_object("cloudcores", "myclouds")
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>()
----> 1
      2
      3
      4
      5

/1/home/taskere/yt/yt/data_objects/data_containers.py in 
save_object(self, name, filename)
    329         """
    330         if filename is not None:
--> 331             ds = shelve.open(filename, protocol=-1)
    332             if name in ds:
    333                 mylog.info("Overwriting %s in %s", name, filename)

NameError: global name 'shelve' is not defined

(I added in an 'import shelve' for good measure, but it didn't help).

Finally, I tried:

In [18]: cloudcores.save_object("myclouds", "cloudstored.cpkl")
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/1/home/taskere/yt/scripts/iyt in <module>()
----> 1
      2
      3
      4
      5

AttributeError: 'dict' object has no attribute 'save_object'


Thanks once again,

Elizabeth




Matthew Turk wrote:
> It might also be worthwhile to see what, exactly, core is ...
>
> print core
>
> Depending on how it is loaded/unloaded, it might be a tuple of the
> parameter file, or might be something slightly other than you are
> expecting.  This comes about because it tries really hard to make sure
> that the parameter file doesn't disappear.
>
> -Matt
>
> On Thu, Aug 11, 2011 at 9:20 AM, Stephen Skory <s at skory.us> wrote:
>   
>> Elizabeth,
>>
>> have you tried using the yt-approved object storage?
>>
>> http://yt.enzotools.org/doc/analyzing/objects.html?#storing-and-loading-objects
>>
>> On Thu, Aug 11, 2011 at 9:09 AM, Elizabeth Tasker <taskere at mcmaster.ca> wrote:
>>     
>>> Hi,
>>>
>>> (Another day a different problem!): I'd like to pickle the results from
>>> extract_connected_sets, but I can't seem to retrieve what I pickle properly.
>>> I have:
>>>
>>> contours = dd.extract_connected_sets("NegEscapeVelocity", 1, 30.0, maxv,
>>> log_space=False)
>>> cloudcores = contours[1][0] #cores defined by contour 0
>>>
>>> file = open('testa.pickle','wb')
>>> cPickle.dump(cloudcores,file,protocol=-1)
>>> file.close()
>>>
>>> file = open('testa.pickle','rb')
>>> core = cPickle.load(file)
>>> file.close()
>>>
>>> But while:
>>>
>>> In [76]: cloudcores[40]["Density"]
>>> Out[76]:
>>> array([  3.80336226e-23,   4.31254788e-23,   3.87927154e-23, ...,
>>>        1.26533774e-22,   2.13753864e-22,   2.74680682e-22])
>>>
>>>
>>>
>>> In [77]: core[40]["Density"]
>>> ---------------------------------------------------------------------------
>>> KeyError                                  Traceback (most recent call last)
>>>
>>> /1/home/taskere/yt/scripts/iyt in <module>()
>>> ----> 1
>>>     2
>>>     3
>>>     4
>>>     5
>>>
>>> KeyError: 40
>>>
>>>
>>> Is it not possible to pickle a contour object or is there something else I
>>> have to do when un-pickling?
>>>
>>> Thank you,
>>>
>>> Elizabeth
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>       
>>
>> --
>> Stephen Skory
>> s at skory.us
>> http://stephenskory.com/
>> 510.621.3687 (google voice)
>> _______________________________________________
>> yt-users mailing list
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>>
>>     
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