[Numpy-discussion] Fortran order in recarray.
Alex Rogozhnikov
alex.rogozhnikov at yandex.ru
Wed Feb 22 11:57:57 EST 2017
Hi Matthew,
maybe it is not the best place to discuss problems of pandas, but to show that I am not missing something, let's consider a simple example.
# simplest DataFrame
x = pandas.DataFrame(dict(a=numpy.arange(10), b=numpy.arange(10, 20)))
# simplest indexing. Can you predict results without looking at comments?
x[:2] # returns two first rows, as expected
x[[0, 1]] # returns copy of x, whole dataframe
x[numpy.array(2)] # fails with IndexError: indices are out-of-bounds (can you guess why?)
x[[0, 1], :] # unhashable type: list
just in case - I know about .loc and .iloc, but when you write code with many subroutines, you concentrate on numpy inputs, and at some point you simply forget to convert some of the data you operated with to numpy and it continues to work, but it yields wrong results (while you tested everything, but you tested this for numpy). Checking all the inputs in each small subroutine is strange.
Ok, a bit more:
x[x['a'] > 5] # works as expected
x[x['a'] > 5, :] # 'Series' objects are mutable, thus they cannot be hashed
lookup = numpy.arange(10)
x[lookup[x['a']] > 5] # works as expected
x[lookup[x['a']] > 5, :] # TypeError: unhashable type: 'numpy.ndarray'
x[lookup]['a'] # indexError
x['a'][lookup] # works as expected
Now let's go a bit further: train/test splitted the data for machine learning (again, the most frequent operation)
from sklearn.model_selection import train_test_split
x1, x2 = train_test_split(x, random_state=42)
# compare next to operations with pandas.DataFrame
col = x1['a']
print col[:2] # first two elements
print col[[0, 1]] # doesn't fail (while there in no row with index 0), fills it with NaN
print col[numpy.arange(2)] # same as previous
print col[col > 4] # as expected
print col[col.values > 4] # as expected
print col.values[col > 4] # converts boolean to int, uses int indexing, but at least raises warning
Mistakes done by such silent misoperating are not easy to detect (when your data pipeline consists of several steps), quite hard to locate the source of problem and almost impossible to be sure that you indeed avoided all such caveats. Code review turns into paranoidal process (if you care about the result, of course).
Things are even worse, because I've demonstrated this for my installation, and probably if you run this with some other pandas installation, you get some other results (that were really basic operations). So things that worked ok in one version, may work different way in the other, this becomes completely intractable.
Pandas may be nice, if you need a report, and you need get it done tomorrow. Then you'll throw away the code. When we initially used pandas as main data storage in yandex/rep, it looked like an good idea, but a year later it was obvious this was a wrong decision. In case when you build data pipeline / research that should be working several years later (using some other installation by someone else), usage of pandas shall be minimal.
That's why I am looking for a reliable pandas substitute, which should be:
- completely consistent with numpy and should fail when this wasn't implemented / impossible
- fewer new abstractions, nobody wants to learn one-more-way-to-manipulate-the-data, specifically other researchers
- it may be less convenient for interactive data mungling
- in particular, less methods is ok
- written code should be interpretable, and hardly can be misinterpreted.
- not super slow, 1-10 gigabytes datasets are a normal situation
Well, that's it.
Sorry for large letter.
Alex.
> 22 февр. 2017 г., в 18:38, Matthew Harrigan <harrigan.matthew at gmail.com> написал(а):
>
> Alex,
>
> Can you please post some code showing exactly what you are trying to do and any issues you are having, particularly the "irritating problems with its row indexing and some other problems" you quote above?
>
> On Wed, Feb 22, 2017 at 10:34 AM, Robert McLeod <robbmcleod at gmail.com <mailto:robbmcleod at gmail.com>> wrote:
> Just as a note, Appveyor supports uploading modules to "public websites":
>
> https://packaging.python.org/appveyor/ <https://packaging.python.org/appveyor/>
>
> The main issue I would see from this, is the PyPi has my password stored on my machine in a plain text file. I'm not sure whether there's a way to provide Appveyor with a SSH key instead.
>
> On Wed, Feb 22, 2017 at 4:23 PM, Alex Rogozhnikov <alex.rogozhnikov at yandex.ru <mailto:alex.rogozhnikov at yandex.ru>> wrote:
> Hi Francesc,
> thanks a lot for you reply and for your impressive job on bcolz!
>
> Bcolz seems to make stress on compression, which is not of much interest for me, but the ctable, and chunked operations look very appropriate to me now. (Of course, I'll need to test it much before I can say this for sure, that's current impression).
>
> The strongest concern with bcolz so far is that it seems to be completely non-trivial to install on windows systems, while pip provides binaries for most (or all?) OS for numpy.
> I didn't build pip binary wheels myself, but is it hard / impossible to cook pip-installabel binaries?
>
>> You can change shapes of numpy arrays, but that usually involves copies of the whole container.
> sure, but this is ok for me, as I plan to organize column editing in 'batches', so this should require seldom copying.
> It would be nice to see an example to understand how deep I need to go inside numpy.
>
> Cheers,
> Alex.
>
>
>
>
>> 22 февр. 2017 г., в 17:03, Francesc Alted <faltet at gmail.com <mailto:faltet at gmail.com>> написал(а):
>>
>> Hi Alex,
>>
>> 2017-02-22 12:45 GMT+01:00 Alex Rogozhnikov <alex.rogozhnikov at yandex.ru <mailto:alex.rogozhnikov at yandex.ru>>:
>> Hi Nathaniel,
>>
>>
>>> pandas
>>
>> yup, the idea was to have minimal pandas.DataFrame-like storage (which I was using for a long time),
>> but without irritating problems with its row indexing and some other problems like interaction with matplotlib.
>>
>>> A dict of arrays?
>>
>>
>> that's what I've started from and implemented, but at some point I decided that I'm reinventing the wheel and numpy has something already. In principle, I can ignore this 'column-oriented' storage requirement, but potentially it may turn out to be quite slow-ish if dtype's size is large.
>>
>> Suggestions are welcome.
>>
>> You may want to try bcolz:
>>
>> https://github.com/Blosc/bcolz <https://github.com/Blosc/bcolz>
>>
>> bcolz is a columnar storage, basically as you require, but data is compressed by default even when stored in-memory (although you can disable compression if you want to).
>>
>>
>>
>> Another strange question:
>> in general, it is considered that once numpy.array is created, it's shape not changed.
>> But if i want to keep the same recarray and change it's dtype and/or shape, is there a way to do this?
>>
>> You can change shapes of numpy arrays, but that usually involves copies of the whole container. With bcolz you can change length and add/del columns without copies. If your containers are large, it is better to inform bcolz on its final estimated size. See:
>>
>> http://bcolz.blosc.org/en/latest/opt-tips.html <http://bcolz.blosc.org/en/latest/opt-tips.html>
>>
>> Francesc
>>
>>
>> Thanks,
>> Alex.
>>
>>
>>
>>> 22 февр. 2017 г., в 3:53, Nathaniel Smith <njs at pobox.com <mailto:njs at pobox.com>> написал(а):
>>>
>>> On Feb 21, 2017 3:24 PM, "Alex Rogozhnikov" <alex.rogozhnikov at yandex.ru <mailto:alex.rogozhnikov at yandex.ru>> wrote:
>>> Ah, got it. Thanks, Chris!
>>> I thought recarray can be only one-dimensional (like tables with named columns).
>>>
>>> Maybe it's better to ask directly what I was looking for:
>>> something that works like a table with named columns (but no labelling for rows), and keeps data (of different dtypes) in a column-by-column way (and this is numpy, not pandas).
>>>
>>> Is there such a magic thing?
>>>
>>> Well, that's what pandas is for...
>>>
>>> A dict of arrays?
>>>
>>> -n
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>>
>> --
>> Francesc Alted
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> Center for Cellular Imaging and Nano Analytics (C-CINA)
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