[yt-dev] [Bug] Halo Catalog units

Nathan Goldbaum nathan12343 at gmail.com
Thu Jun 2 12:15:21 PDT 2016 

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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