[yt-dev] [Bug] Halo Catalog units

Britton Smith brittonsmith at gmail.com
Mon Jun 13 09:38:40 PDT 2016


Hi Rasmi,

My apologies for not responding earlier to this.  I have been away on
holiday the last two weeks and didn't see this.

Back when the HaloCatalog was first implemented, the .to_json and
.from_json functions for saving and loading unit registries did not exist,
or I was not aware of them.  To avoid confusion, I simply converted all
fields to CGS for saving.  You can see this around line 435 (in the ._run
function) of halo_catalog.py.  This is why code_length and CGS units are
the same for HaloCatalogDatasets.

I'm looking over your PR write now and will leave additional comments there.

Britton

On Thu, Jun 2, 2016 at 8:50 PM, Rasmi Elasmar <re2300 at columbia.edu> wrote:

> Makes sense! PR submitted
> <https://bitbucket.org/yt_analysis/yt/pull-requests/2208/added-halo-catalog-unit_registry-saving/diff>
> -- let me know if that's good. Thanks for your help!
>
> On Thu, Jun 2, 2016 at 3:15 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Thu, Jun 2, 2016 at 2:05 PM, Rasmi Elasmar <re2300 at columbia.edu>
>> wrote:
>>
>>> Nathan,
>>>
>>> Sorry for the excess of questions. Should I implement the unit_registry
>>> attr check here
>>> <https://bitbucket.org/yt_analysis/yt/src/b8a09cd382dd34f386ce3634e7f78df3f5d9401d/yt/data_objects/static_output.py?at=yt&fileviewer=file-view-default#static_output.py-802>?
>>> If so, how can I access the h5 dataset from there? If not, is here
>>> <https://bitbucket.org/yt_analysis/yt/src/b8a09cd382dd34f386ce3634e7f78df3f5d9401d/yt/frontends/halo_catalog/data_structures.py?at=yt&fileviewer=file-view-default#data_structures.py-32>
>>> better?
>>>
>>
>> I would do it inside the `HaloCatalogDataset` class.
>>
>>
>>> I don't know what the order of precedence is, so I don't want the
>>> creation of the unit registry to be overwritten by the default one
>>> _create_unit_registry call in the Dataset __init__. Is Particle File being
>>> passed a Dataset that is already initiated with the default UnitRegistry?
>>>
>>
>> You could add an implementation of _create_unit_regsitry to
>> `HaloCatalogDataset` that supplements the implementation in the base class.
>> First, call the superclass implementation, then if a registry is available
>> in the output file, overwrite it inside `HaloCatalogDataset`. Something
>> like this (using pseudocode here):
>>
>>     class HaloCatalogDataset(Dataset)
>>
>>     ... snip stuff that's already in this class ....
>>
>>         def _create_unit_registry(self):
>>              super(HaloCatalogDataset, self)._create_unit_registry()
>>              if registry in output_file:
>>                   # replace the registry with what's in the output file
>>
>> -Nathan
>>
>>
>>> On Thu, Jun 2, 2016 at 2:18 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Thu, Jun 2, 2016 at 1:16 PM, Rasmi Elasmar <re2300 at columbia.edu>
>>>> wrote:
>>>>
>>>>> Hi Nathan,
>>>>>
>>>>> That approach sounds good. What do you think about this implementation?
>>>>>
>>>>>> import h5py
>>>>>> import yt
>>>>>
>>>>>
>>>>>
>>>>> ds = yt.load('RD0009/RD0009')
>>>>>> hc_file = h5py.File('halo_catalogs/catalog/catalog.0.h5')
>>>>>
>>>>>
>>>>>
>>>>> # Include unit_registry as an attribute
>>>>>> hc_file.attrs['unit_registry'] = ds.unit_registry.to_json()
>>>>>
>>>>>
>>>>>
>>>>> # Or as a string dataset
>>>>>> unit_registry_json = ds.unit_registry.to_json()
>>>>>> str_type = h5py.special_dtype(vlen=str)
>>>>>> unit_registry_h5 = hcfile.create_dataset('unit_registry_json',
>>>>>> shape=(1,), dtype=str_type)
>>>>>> unit_registry_h5[:] = unit_registry_json
>>>>>
>>>>>
>>>>>
>>>>> hc_file.close()
>>>>>
>>>>>
>>>>>
>>>>> # Regenerate unit_registry when loading the HaloCatalog?
>>>>>> halos_ds = yt.load('halo_catalogs/catalog/catalog.0.h5')
>>>>>> hc_file = h5py.File('halo_catalogs/catalog/catalog.0.h5')
>>>>>> unit_registry_json = hc_file.attrs['unit_registry']
>>>>>> halos_ds.unit_registry =
>>>>>> yt.units.unit_registry.UnitRegistry.from_json(unit_registry_json)
>>>>>
>>>>>
>>>>>
>>>>> I'm not sure if including the unit_registry as an attribute or string
>>>>> dataset is a better idea -- it seems to be an attribute in other
>>>>> parts of the codebase
>>>>> <https://bitbucket.org/yt_analysis/yt/src/c117d528f18ea412f8b80e8522a0595444e20ae8/yt/units/yt_array.py?at=yt&fileviewer=file-view-default#yt_array.py-796>
>>>>> .
>>>>>
>>>>
>>>> Either should be fine. I've actually been meaning to update the snippet
>>>> you linked to use the JSON method, since pickles aren't portable across
>>>> python versions, but we need to be careful to maintain backward
>>>> compatibility with older files.
>>>>
>>>>
>>>>>
>>>>> Then, how do we get it to take the place of the halos_ds
>>>>> unit_registry? Should this be done on creation in HaloCatalogDataset
>>>>> <https://bitbucket.org/yt_analysis/yt/src/b8a09cd382dd34f386ce3634e7f78df3f5d9401d/yt/frontends/halo_catalog/data_structures.py?at=yt&fileviewer=file-view-default#data_structures.py-40>?
>>>>> (i.e., check if the h5 file has a unit_registry attr, if so, load that, if
>>>>> not use the current defaults?)
>>>>>
>>>>>
>>>> Sounds good! Looking forward to the pull request that implements this.
>>>>
>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Rasmi
>>>>>
>>>>> On Wed, Jun 1, 2016 at 1:01 PM, Nathan Goldbaum <nathan12343 at gmail.com
>>>>> > wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Jun 1, 2016 at 11:40 AM, Rasmi Elasmar <re2300 at columbia.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> Greg and I found a bug involving halo catalog unit handling:
>>>>>>>
>>>>>>> >>> halo.quantities['particle_position_x']
>>>>>>>> 0.495074982741 cm
>>>>>>>> >>> halo.quantities['particle_position_x'].in_units('code_length')
>>>>>>>> 0.495074982741 code_length
>>>>>>>> >>> halo.quantities['particle_position_x'].in_units('cm')
>>>>>>>> 0.495074982741 cm
>>>>>>>> >>> ds.unit_registry['code_length']
>>>>>>>> (9.195880139956267e+25, (length))
>>>>>>>> >>> halos_ds.unit_registry['code_length']
>>>>>>>> (1.0, (length))
>>>>>>>
>>>>>>>
>>>>>>> The halos_ds mixes up cm and code_length units when the HaloCatalog
>>>>>>> object is created from a saved halo catalog. The halo catalog values are
>>>>>>> saved in code_length, but the HaloCatalog object assumes they are in cm.
>>>>>>>
>>>>>>> Here
>>>>>>> <https://bitbucket.org/yt_analysis/yt/src/b8a09cd382dd34f386ce3634e7f78df3f5d9401d/yt/analysis_modules/halo_analysis/halo_catalog.py?at=yt&fileviewer=file-view-default#halo_catalog.py-453>
>>>>>>> is where the code_length units are written out after halo-finding is done
>>>>>>> (this is confirmed with an h5ls).
>>>>>>> Here is where the halos_ds
>>>>>>> <https://bitbucket.org/yt_analysis/yt/src/b8a09cd382dd34f386ce3634e7f78df3f5d9401d/yt/frontends/halo_catalog/data_structures.py?at=yt&fileviewer=file-view-default#data_structures.py-78> for
>>>>>>> the HaloCatalog is created. The length unit is set in cm -- the catalog is
>>>>>>> assumed to be in cgs.
>>>>>>> The HaloCatalog fields
>>>>>>> <https://bitbucket.org/yt_analysis/yt/src/b8a09cd382dd34f386ce3634e7f78df3f5d9401d/yt/frontends/halo_catalog/fields.py?at=yt&fileviewer=file-view-default#fields.py-21>
>>>>>>> also assume cgs.
>>>>>>>
>>>>>>> In theory, the HaloCatalog could just parse the code_length units of
>>>>>>> the halos_ds, but this isn't necessarily known at the time of creation, so
>>>>>>> the ideal fix may be to save the halo catalog length units in cm instead of
>>>>>>> in code_length. Then the assumptions that are made about length being in cm
>>>>>>> when creating a HaloCatalog object from a halo catalog would be correct.
>>>>>>> Any thoughts on this approach or other approaches?
>>>>>>>
>>>>>>>
>>>>>> It would probably be better just to save the unit registry into the
>>>>>> hdf5 file. You might find the UnitRegistry.to_json() and
>>>>>> UnitRegistry.from_json() to be useful here - the json data could be saved
>>>>>> in the HDF5 output file as a string dataset.
>>>>>>
>>>>>>
>>>>>> https://bitbucket.org/yt_analysis/yt/src/yt/yt/units/unit_registry.py?at=yt&fileviewer=file-view-default#unit_registry.py-120
>>>>>>
>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Rasmi
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
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