[yt-users] unpickle / load problems

[Elizabeth Tasker]

Hi Matt,

According to the directory I have in yt, an older version:

/Users/Elizabeth/yt/src/h5py-2.0.1/

Elizabeth

On Mar 15, 2013, at 10:04 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Elizabeth,
> 
> On Wed, Mar 13, 2013 at 4:45 PM, Elizabeth Tasker
> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>> Hi Matt,
>> 
>> So ironically, it took me a long time to find the right combination to make this break in the test script! The fatal combination seems to be an extract region from a boolean object.
>> 
>> This is the script I used:
>> 
>> http://paste.yt-project.org/show/3228/
>> 
>> It should work with any data set.
>> 
>> It creates 6 saved objects. Objects 1-4 work fine but 5 and 6 have the attribute error.
> 
> I'm getting h5py errors when I even run the script.  Which version of
> h5py are you on?
> 
>>>> h5py.version.version
> '2.1.0'
> 
> 
>> 
>> Elizabeth
>> 
>> 
>> On Mar 13, 2013, at 3:08 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>> 
>>> Hi Elizabeth,
>>> 
>>> Okay, this seems like it's bumped up against a problem with the way yt
>>> handles pickles.  At some point in the reconstruction, data objects
>>> aren't getting separated from their parameter files.
>>> 
>>> Any chance you could make something that reproduces this on one of the
>>> workshop datasets?
>>> 
>>> http://yt-project.org/data/
>>> 
>>> -Matt
>>> 
>>> On Wed, Mar 13, 2013 at 3:03 PM, Elizabeth Tasker
>>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>>> Hi,
>>>> 
>>>> I'm struggling to unpickle / load_object a previously pickled / save_object.
>>>> 
>>>> I've done:
>>>> 
>>>> pf.h.save_object(allclouds, "clouds_pyfindclouds2_yt")
>>>> 
>>>> but when I do:
>>>> 
>>>> clouds = pf.h.load_object("clouds_pyfindclouds2_yt")
>>>> 
>>>> I get:
>>>> 
>>>> AttributeError                            Traceback (most recent call last)
>>>> /Users/Elizabeth/yt/src/yt-hg/scripts/iyt in <module>()
>>>> ----> 1 execfile("cloud_surfacedensity_b.py")
>>>> 
>>>> /Users/Elizabeth/yt/src/yt-hg/scripts/iyt in <module>()
>>>>    13 #file.close()
>>>>    14
>>>> ---> 15 clouds = pf.h.load_object("clouds_pyfindclouds2_yt")
>>>> 
>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/hierarchy.pyc in load_object(self, name)
>>>>   328         if obj is None:
>>>>   329             return
>>>> --> 330         obj = cPickle.loads(obj.value)
>>>>   331         if iterable(obj) and len(obj) == 2:
>>>>   332             obj = obj[1] # Just the object, not the pf
>>>> 
>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/data_containers.pyc in _reconstruct_object(*args, **kwargs)
>>>>  4623     pf = pfs.get_pf_hash(pfid)
>>>>  4624     cls = getattr(pf.h, dtype)
>>>> -> 4625     obj = cls(*new_args)
>>>>  4626     obj.field_parameters.update(field_parameters)
>>>>  4627     return pf, obj
>>>> 
>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, regions, fields, pf, **kwargs)
>>>>  4046         self._all_overlap = []
>>>>  4047         self._cut_masks = {}
>>>> -> 4048         self._get_all_regions()
>>>>  4049         self._make_overlaps()
>>>>  4050         self._get_list_of_grids()
>>>> 
>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/data_containers.pyc in _get_all_regions(self)
>>>>  4057             self._all_regions.append(item)
>>>>  4058             # So cut_masks don't get messed up.
>>>> -> 4059             item._boolean_touched = True
>>>>  4060         self._all_regions = np.unique(self._all_regions)
>>>>  4061
>>>> 
>>>> AttributeError: ("'tuple' object has no attribute '_boolean_touched'", <function _reconstruct_object at 0x101dcd578>, ('73850deee907adf5217f43156c5057cd', 'boolean', [(GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240, AMRCylinder (GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240): center=[ 16.  16.  16.], _norm_vec=[ 0.  0.  1.], _radius=7.5, _height=0.100000208264), 'NOT', (GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240, AMRCylinder (GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240): center=[ 16.  16.  16.], _norm_vec=[ 0.  0.  1.], _radius=4.5, _height=0.100000208264)], {'bulk_velocity': array([ 0.,  0.,  0.]), 'center': array([ 0.5,  0.5,  0.5]), 'normal': array([ 0.,  0.,  1.])}))
>>>> 
>>>> 
>>>> 
>>>> This is all on the same computer.
>>>> 
>>>> Elizabeth
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