[TEP002] Add a to_hdf method to the Radial1DModel

[ftsamis]

Added a model.to_hdf method which in turn calls plasma.to_hdf and also stores t_inner, ws, t_rads, v_inner, v_outer.

Additionally, atom_data_uuid is also stored in a Series under the HDF structure path model/metadata.

[wkerzendorf]

remove this - runner will be stored as part of simulation

[yeganer]

May I suggest creating one Dataframe (called properties or smth) and then adding the numpy arrays as columns?

[ftsamis]

Yeah, I hadn't noticed that they are all the same length. Is that always the case? Because otherwise this won't work.

[yeganer]

Are they exactly the same length? I don't know but it's not important. If
one element is longer than the rest the others get filled with np.nan. One
would have to take care of that when reading the valus, that's all

Fotis Tsamis notifications@github.com schrieb am Mo., 20. Juni 2016 um
17:18 Uhr:

In tardis/model.py
#589 (comment):

@@ -268,6 +268,16 @@ def to_hdf(self, path_or_buf, path='', plasma_properties=None):
None

     """

•    properties = ['t_inner', 'ws', 't_rads', 'v_inner', 'v_outer']
  

•    for p in properties:
  

•        output_value = getattr(self, p)
  

•        if hasattr(output_value, 'si'):
  

•            output_value = output_value.si.value
  

•        if np.isscalar(output_value):
  

•            output_value = [output_value]
  

•        data = pd.DataFrame(output_value)
  

Yeah, I hadn't noticed that they are all the same length. Is that always
the case? Because otherwise this won't work.

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[ftsamis]

As far as I checked it does not do that automatically.

>>>pd.DataFrame({'a': [1,2], 'b' : [1,2,3]})
ValueError: arrays must all be same length

while:

>>> pd.DataFrame({'a': [1,2], 'b' : [1,2]})
   a  b
0  1  1
1  2  2

So one would have to take care of manually adding np.nan for the missing values of shorter columns as well.

[yeganer]

You want to do it this way:

df = pd.DataFrame()
df['a'] = [1,2,3]
df['b'] = [1,2]

Fotis Tsamis notifications@github.com schrieb am Mo., 20. Juni 2016 um
18:56 Uhr:

In tardis/model.py
#589 (comment):

@@ -268,6 +268,16 @@ def to_hdf(self, path_or_buf, path='', plasma_properties=None):
None

     """

•    properties = ['t_inner', 'ws', 't_rads', 'v_inner', 'v_outer']
  

•    for p in properties:
  

•        output_value = getattr(self, p)
  

•        if hasattr(output_value, 'si'):
  

•            output_value = output_value.si.value
  

•        if np.isscalar(output_value):
  

•            output_value = [output_value]
  

•        data = pd.DataFrame(output_value)
  

As far as I checked it does not do that automatically.

pd.DataFrame({'a': [1,2], 'b' : [1,2,3]})ValueError: arrays must all be same length

while:

pd.DataFrame({'a': [1,2], 'b' : [1,2]})
a b0 1 11 2 2

So one would have to take care of manually adding np.nan for the missing
values of shorter columns as well.

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[ftsamis]

That was unexpected to me. Alright, thanks for pointing this out.

[ftsamis]

Are you sure this works? Because the exact snippet you gave throws a ValueError: Length of values does not match length of index for me.

[wkerzendorf]

I think there is a high likelihood that this doesn't work. But all of the values in model have the same length.

[ftsamis]

I was actually trying to do the same with the plasma properties, so we could have a uniform way of storing things.

[wkerzendorf]

@tardis-sn/tardis-core can someone else look at this - from my point of view it looks mergeable.

[ftsamis]

Note to self: After this is merged, I should rebase #601 on to_hdf and change the plasma.to_hdf call which is made in the model.to_hdf to match the new signature.

[wkerzendorf]

@tardis-sn/tardis-core looks good to me - should we merge?

[ftsamis]

I think we should merge this, since either way it's going to face some minor changes because of some additions to the way data are stored to HDF in #601. Then, when both this and #601 are merged we can discuss if we are happy to merge the entire to_hdf branch to master. For now, this also blocks #601 from having its couple last commits.