[yt-users] Another clump finder error

[Britton Smith]

Hi Caroline,

There are two separate things happening here.  The first is that
serializing data objects, which is what the save_object call is doing, was
disabled as the default behavior a while back.  Fortunately, you can enable
this by adding the following at the very top of your script:
from yt.config import ytcfg
ytcfg['yt', 'serialize'] = 'True'

Note, this needs to go above "from yt.mods import *" or any other yt
imports you may do.

The second part is that, when enabled, this functionality appears to be
broken.  I did a quick test myself with the clump finder using the cookbook
script (after I added the above lines) and got the following error while
trying to reload the object:

Traceback (most recent call last):
  File "find_clumps.py", line 71, in <module>
    master_clump = pf.h.load_object('My_clumps')
  File
"/Users/britton/Documents/work/yt/yt-2.x/src/yt-hg/yt/data_objects/hierarchy.py",
line 322, in load_object
    obj = cPickle.loads(obj.value)
AttributeError: 'numpy.ndarray' object has no attribute 'value'

I do not think this is terribly difficult to fix.  Matt, can you comment on
this?

Sorry for the troubles!

Britton


On Tue, Jan 21, 2014 at 3:54 PM, Caroline Van Borm <borm at astro.rug.nl>wrote:

> Hi all,
>
> I just wanted to add to this that I also tried to save my clump object
> (called master_clump) using <master_clump.save_object("myclumps",
> "myclumpsfile.cpkl")>. However, this gives the error: "AttributeError:
> 'Clump' object has no attribute 'save_object'". It is very inconvenient
> that I cannot save the clump object, as the clump finding takes quite long.
> Any ideas?
>
> Thank you!
>
> Cheers,
> Caroline
>
>
>
> On 17-Jan-14 14:16, Caroline Van Borm wrote:
>
>> Hi all,
>>
>> Sorry to bother you again, but I have another problem with the clump
>> finder. I have been able to run the script to find the clumps, wrote them
>> to a text file, and saved the clump object using <pf.h.save_object(master_clump,
>> 'myclumps')>. However, when I try to read the object back in and get the
>> lowest clumps using
>>
>>     master_clump = pf.h.load_object('myclumps')
>>     leaf_clumps = get_lowest_clumps(master_clump)
>>
>> I get an error saying:
>>     Traceback (most recent call last):
>>       File "./findclumps.py", line 66, in <module>
>>         leaf_clumps = get_lowest_clumps(master_clump)
>>       File "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_
>> modules/level_sets/clump_handling.py", line 209, in get_lowest_clumps
>>         if clump.children is None or len(clump.children) == 0:
>>     AttributeError: 'NoneType' object has no attribute 'children'
>>
>> Does this happen because the clump object didn't actually get saved? And
>> how can I check whether it did or not?
>>
>> Thanks again!
>>
>> Cheers,
>> Caroline
>> _______________________________________________
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>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
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