[yt-users] pickle
Elizabeth Tasker
tasker at astro1.sci.hokudai.ac.jp
Thu Dec 1 06:32:28 PST 2011
Sorry, still no luck!
The current version of the code is:
---
c1a446be3a7a (yt) tip
---
unpickle core data
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/home/taskere/yt-2/src/yt-hg/scripts/iyt in <module>()
199
200 file = open('cores.pickle','rb')
--> 201 allcloudcores = cPickle.load(file)
202 file.close()
203
/home/taskere/yt-2/src/yt-hg/yt/data_objects/data_containers.pyc in _reconstruct_object(*args, **kwargs)
3640 else: new_args.append(arg)
3641 pfs = ParameterFileStore()
-> 3642 pf = pfs.get_pf_hash(pfid)
3643 cls = getattr(pf.h, dtype)
3644 obj = cls(*new_args)
/home/taskere/yt-2/src/yt-hg/yt/utilities/parameter_file_storage.pyc in get_pf_hash(self, hash)
109 def get_pf_hash(self, hash):
110 """ This returns a parameter file based on a hash. """
--> 111 return self._convert_pf(self._records[hash])
112
113 def get_pf_ctid(self, ctid):
KeyError: (('283b7c4d88671dbff7acf083098da6ae',), <function _reconstruct_object at 0xa8cd848>, ('283b7c4d88671dbff7acf083098da6ae', 'region', array([ 16., 16., 16.]), array([ 0., 0., 0.]), array([ 32., 32., 32.]), {'disk_center': array([16, 16, 16]), 'center': array([ 16., 16., 16.]), 'bulk_velocity': array([ 0., 0., 0.]), 'disk_vector': array([0, 0, 1]), 'disk_radius': array([ 0.1 , 0.1238, 0.1476, 0.1714, 0.1952, 0.219 ,
0.2428, 0.2666, 0.2904, 0.3142, 0.33
Unless I need to re-pickle first?
Elizabeth
On 2011-12-01, at 8:20 PM, Matthew Turk wrote:
> Thanks, Elizabeth. The move to in-memory brought up a funny bug where
> the initialization process was reseting the list of known parameter
> hashes. This is fixed in c1a446be3a7a.
>
> Also, save_object won't work except on yt objects; the result of
> extract_connected_sets is a tuple of values and python objects.
> Pickle will, tho.
>
> On Thu, Dec 1, 2011 at 4:33 AM, Elizabeth Tasker
> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>> I also tried switching out pickle for the yt method of storing
>> objects. Unfortunately, it doesn't seem to save the object I want. I
>> tried:
>>
>> contours = dd.extract_connected_sets("NegEscapeVelocity", 1, 30.0,
>> maxv, log_space=False)
>> contours.save_object("cloudcores", "storedcores.cpkl")
>>
>> In [1]: contours.save_object("cloudcores", "storedcores.cpkl")
>> ---------------------------------------------------------------------------
>> AttributeError Traceback (most recent call last)
>>
>> /home/tasker/yt/src/yt-hg/scripts/iyt in <module>()
>> ----> 1
>> 2
>> 3
>> 4
>> 5
>>
>> AttributeError: 'tuple' object has no attribute 'save_object'
>>
>> The alternative method --of saving it via the hierarchy-- is slightly
>> less good since I'm running multiple yt scripts on the same data set.
>> (As least, when I tried to load the values back in, it produced an
>> empty set which I presume was because I'd inadvertently overwritten
>> the .yt file?).
>>
>> If I could get one of these working again, then I'd be super happy. I
>> don't need the all :)
>>
>> Elizabeth
>>
>>
>> On 1 December 2011 12:35, Elizabeth Tasker
>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>> Hi Matt,
>>>
>>> Sorry, that still doesn't work.... unless I've misunderstood your
>>> suggestion? The code is here:
>>>
>>> http://paste.yt-project.org/show/1974/
>>>
>>> Pickle + unpickle on a pile of properties I calculate from the
>>> connected sets is fine, but pickling the connected sets themselves is
>>> a problem. Could it be the later pickle doesn't require the parameter
>>> file? Or is it possible there is an unrelated write error happening?
>>>
>>> Elizabeth
>>>
>>> On 30 November 2011 23:43, Matthew Turk <matthewturk at gmail.com> wrote:
>>>> Hi Elizabeth,
>>>>
>>>> We recently changed the mechanism of storing parameter files to be
>>>> off-by-default, which means that rather than dumping them to a .csv
>>>> file, they only stay in memory. This functionality can be turned back
>>>> on (this change is documented in the development documentation.) Can
>>>> you try:
>>>>
>>>> 1) Loading your parameter file, *then* loading your pickle. I am
>>>> optimistic this will fix it.
>>>> 2) If it doesn't, at the very top of your python script, put this:
>>>>
>>>> from yt.config import ytcfg; ytcfg["yt","storeparameterfiles"] = "True"
>>>>
>>>> -Matt
>>>>
>>>> On Wed, Nov 30, 2011 at 4:46 AM, Elizabeth Tasker
>>>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>>>> Hi,
>>>>>
>>>>> A bigger problem....
>>>>>
>>>>> The lastest version of yt
>>>>>
>>>>> The current version of the code is:
>>>>>
>>>>> ---
>>>>> a519b8754ba8 (yt) tip
>>>>> ---
>>>>>
>>>>>
>>>>> has problems with pickle. If I pickle a data set and then try and
>>>>> unpickle it, I see:
>>>>>
>>>>> unpickle core data
>>>>> ---------------------------------------------------------------------------
>>>>> KeyError Traceback (most recent call last)
>>>>>
>>>>> /home/tasker/yt/src/yt-hg/scripts/iyt in <module>()
>>>>> 338
>>>>> 339 #file = open('cores.pickle','rb')
>>>>> --> 340 allcloudcores = cPickle.load(file('cores.pickle', 'rb'))
>>>>> 341 file.close()
>>>>> 342
>>>>>
>>>>> /home/tasker/yt/src/yt-hg/yt/data_objects/data_containers.pyc in
>>>>> _reconstruct_object(*args, **kwargs)
>>>>> 3676 else: new_args.append(arg)
>>>>> 3677 pfs = ParameterFileStore()
>>>>> -> 3678 pf = pfs.get_pf_hash(pfid)
>>>>> 3679 cls = getattr(pf.h, dtype)
>>>>> 3680 obj = cls(*new_args)
>>>>>
>>>>> /home/tasker/yt/src/yt-hg/yt/utilities/parameter_file_storage.pyc in
>>>>> get_pf_hash(self, hash)
>>>>> 106 def get_pf_hash(self, hash):
>>>>> 107 """ This returns a parameter file based on a hash. """
>>>>> --> 108 return self._convert_pf(self._records[hash])
>>>>> 109
>>>>> 110 def get_pf_ctid(self, ctid):
>>>>>
>>>>> KeyError: (('283b7c4d88671dbff7acf083098da6ae',), <function
>>>>> _reconstruct_object at 0x272c938>,
>>>>> ('283b7c4d88671dbff7acf083098da6ae', 'region', array([ 16., 16.,
>>>>> 16.]), array([ 0., 0., 0.]), array([ 32., 32., 32.]),
>>>>> {'disk_center': array([16, 16, 16]), 'center': array([ 16., 16.,
>>>>> 16.]), 'bulk_velocity': array([ 0., 0., 0.]), 'disk_vector':
>>>>> array([0, 0, 1]), 'disk_radius': array([ 0.1 , 0.1358, 0.1716,
>>>>> 0.2074, 0.2432, 0.279 ,
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> The fact it mentions the field parameters in the last line, might mean
>>>>> it's an error introduced because of the corrections to them (that I
>>>>> have been demanding!)?
>>>>>
>>>>> The script I have works fine (pickles and all) on yt version:
>>>>>
>>>>> ---
>>>>> 16e8d749a806 (yt) tip
>>>>> ---
>>>>>
>>>>>
>>>>> Elizabeth
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
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